From pmr at ebi.ac.uk Thu Jul 1 08:27:09 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 01 Jul 2004 13:27:09 +0100 Subject: [BiO BB] Getting PDB id from Swissprot entry In-Reply-To: <40E2A745.6030400@csa.iisc.ernet.in> References: <40E2A745.6030400@csa.iisc.ernet.in> Message-ID: <40E4031D.8060108@ebi.ac.uk> Sourangshu Bhattacharya wrote: > Hi, > > Is there a direct way (without reading the protein name from swissprot > and searching in PDB) of getting the PDB id of the protein corresponding > to a particular Swissprot id ? Yes ... SwissProt has a DR (database reference) line that points to the PDB entry (assuming, or course, that there is a solved structure in PDB for that protein). For example, this entry has 3 PDB references. ID AMIC_PSEAE STANDARD; PRT; 384 AA. AC P27017; DT 01-AUG-1992 (Rel. 23, Created) DT 16-OCT-2001 (Rel. 40, Last sequence update) DT 15-JUN-2004 (Rel. 44, Last annotation update) DE Aliphatic amidase expression-regulating protein. GN AMIC OR PA3364. OS Pseudomonas aeruginosa. OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; OC Pseudomonadaceae; Pseudomonas. ..... reference (citation) section skipped ..... CC -!- FUNCTION: Negatively regulates the expression of the aliphatic CC amidase operon. AmiC functions by inhibiting the action of amiR at CC the protein level. It exhibits protein kinase activity. CC -!- SUBUNIT: Homodimer. Forms a complex with amiR. CC -!- DOMAIN: Consists of two beta-alpha-beta domains with a central CC cleft in which the amide binds. CC -------------------------------------------------------------------------- CC This SWISS-PROT entry is copyright. It is produced through a collaboration CC between the Swiss Institute of Bioinformatics and the EMBL outstation - CC the European Bioinformatics Institute. There are no restrictions on its CC use by non-profit institutions as long as its content is in no way CC modified and this statement is not removed. Usage by and for commercial CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ CC or send an email to license at isb-sib.ch). CC -------------------------------------------------------------------------- DR EMBL; X13776; CAA32024.1; -. DR EMBL; AE004758; AAG06752.1; -. DR PIR; C83226; C83226. DR PDB; 1PEA; 03-APR-96. DR PDB; 1QNL; 23-DEC-99. DR PDB; 1QO0; 23-DEC-99. DR InterPro; IPR000709; Leu_Ile_Val_bind. DR PRINTS; PR00337; LEUILEVALBP. KW Transferase; Kinase; Repressor; 3D-structure; Complete proteome; KW Direct protein sequencing. ..... features and sequence skipped ..... Hope that helps, Peter Rice From sourangshu at csa.iisc.ernet.in Thu Jul 1 12:03:02 2004 From: sourangshu at csa.iisc.ernet.in (Sourangshu Bhattacharya) Date: Thu, 01 Jul 2004 21:33:02 +0530 Subject: [BiO BB] Getting PDB id from Swissprot entry In-Reply-To: References: Message-ID: <40E435B6.5020507@csa.iisc.ernet.in> Hi Dan, Thank you very much. I didn't know about MSD. There is also an entry HSSP in swissprot which gives homologues. Sourangshu Dan Bolser wrote: >On Wed, 30 Jun 2004, Sourangshu Bhattacharya wrote: > > > >>Hi, >> >>Is there a direct way (without reading the protein name from swissprot >>and searching in PDB) of getting the PDB id of the protein corresponding >>to a particular Swissprot id ? >> >> > >I would use the MSD database, which maintains a manually curated version >of the SwissProt to PDB mapping. > > > >>Also, how do I know whether structure for a particular protein >>corresponding to a swissprot id has been determined or not ? >> >> > >Strictly speeking, the above mapping gives you this. More realistically, >however, you can consider very close homologues to the above set as also >'solved'. Where you draw the line is a matter of requirement, but you can >get reasonable models (allegedly) at > 40% sequence identity, or >reasonable 'fold prediction' at much larger distances (see SUPERFAMILY for >example). > >It all depends on what you want to do. > > > >>Thank you very much.. >> >>Regards, >>Sourangshu. >> >> >> >> > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- Sourangshu Bhattacharya PhD Student, Dept. of Computer Science & Automation, Indian Institute of Science, Bangalore - 560012, India. Website: http://people.csa.iisc.ernet.in/sourangshu Cell Phone : 91-98457 97492 From sourangshu at csa.iisc.ernet.in Thu Jul 1 12:07:51 2004 From: sourangshu at csa.iisc.ernet.in (Sourangshu Bhattacharya) Date: Thu, 01 Jul 2004 21:37:51 +0530 Subject: [BiO BB] Getting PDB id from Swissprot entry In-Reply-To: <40E4031D.8060108@ebi.ac.uk> References: <40E2A745.6030400@csa.iisc.ernet.in> <40E4031D.8060108@ebi.ac.uk> Message-ID: <40E436D7.6060201@csa.iisc.ernet.in> Hi Peter, Actually I am not working with the Swissprot database files, but only with the web interface. Thank you, Sourangshu Peter Rice wrote: > Sourangshu Bhattacharya wrote: > >> Hi, >> >> Is there a direct way (without reading the protein name from >> swissprot and searching in PDB) of getting the PDB id of the protein >> corresponding to a particular Swissprot id ? > > > Yes ... SwissProt has a DR (database reference) line that points to > the PDB entry (assuming, or course, that there is a solved structure > in PDB for that protein). > > For example, this entry has 3 PDB references. > > ID AMIC_PSEAE STANDARD; PRT; 384 AA. > AC P27017; > DT 01-AUG-1992 (Rel. 23, Created) > DT 16-OCT-2001 (Rel. 40, Last sequence update) > DT 15-JUN-2004 (Rel. 44, Last annotation update) > DE Aliphatic amidase expression-regulating protein. > GN AMIC OR PA3364. > OS Pseudomonas aeruginosa. > OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; > OC Pseudomonadaceae; Pseudomonas. > > ..... reference (citation) section skipped ..... > > > CC -!- FUNCTION: Negatively regulates the expression of the aliphatic > CC amidase operon. AmiC functions by inhibiting the action of > amiR at > CC the protein level. It exhibits protein kinase activity. > CC -!- SUBUNIT: Homodimer. Forms a complex with amiR. > CC -!- DOMAIN: Consists of two beta-alpha-beta domains with a central > CC cleft in which the amide binds. > CC > -------------------------------------------------------------------------- > > CC This SWISS-PROT entry is copyright. It is produced through a > collaboration > CC between the Swiss Institute of Bioinformatics and the EMBL > outstation - > CC the European Bioinformatics Institute. There are no > restrictions on its > CC use by non-profit institutions as long as its content is in > no way > CC modified and this statement is not removed. Usage by and for > commercial > CC entities requires a license agreement (See > http://www.isb-sib.ch/announce/ > CC or send an email to license at isb-sib.ch). > CC > -------------------------------------------------------------------------- > > DR EMBL; X13776; CAA32024.1; -. > DR EMBL; AE004758; AAG06752.1; -. > DR PIR; C83226; C83226. > DR PDB; 1PEA; 03-APR-96. > DR PDB; 1QNL; 23-DEC-99. > DR PDB; 1QO0; 23-DEC-99. > DR InterPro; IPR000709; Leu_Ile_Val_bind. > DR PRINTS; PR00337; LEUILEVALBP. > KW Transferase; Kinase; Repressor; 3D-structure; Complete proteome; > KW Direct protein sequencing. > > ..... features and sequence skipped ..... > > Hope that helps, > > Peter Rice > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Sourangshu Bhattacharya PhD Student, Dept. of Computer Science & Automation, Indian Institute of Science, Bangalore - 560012, India. Website: http://people.csa.iisc.ernet.in/sourangshu Cell Phone : 91-98457 97492 From idoerg at burnham.org Thu Jul 1 12:15:21 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Thu, 01 Jul 2004 09:15:21 -0700 Subject: [BiO BB] Getting PDB id from Swissprot entry In-Reply-To: <40E435B6.5020507@csa.iisc.ernet.in> References: <40E435B6.5020507@csa.iisc.ernet.in> Message-ID: <40E43899.7030103@burnham.org> Hi, I do not know for which particular purpose you are looking for SP <--> PDB mappings, but beware the following perils & pitfalls: 1) The SP <--> PDB mapping can be many-to-many. 1.1 )There may be several entries in PDB which correspond to a single swissprot entry. This is because the same protein may have been structurally solved by different groups at different times, solved with different ligands, point mutated, and so forth. Be very careful about point-mutations: they do not have the same sequence in PDB as in SP. 1.2) At the same time, there may be several SP entries corresponding to a single PDB entry. This may be due to SP redundancy (although database curators are doing a fantastic job of keeping that down), close homologs, or point mutations. 2) An SP amino-acid sequence is rarely the same as the PDB sequence. Usually only part of a structure is solved. Gaps abound, because crystallographers sometimes cannot see the loops. There are large deletions, because there are bits which are not crystallizable, or, if NMR, they are trying to keep the protein short. 3) There are many SP entries which do have an equivalent in PDB, but it does not say so in DR or PDB. See also the "40%" comment below. Cheers, Iddo Sourangshu Bhattacharya wrote: > Hi Dan, > Thank you very much. I didn't know about MSD. > > There is also an entry HSSP in swissprot which gives homologues. > > Sourangshu > > Dan Bolser wrote: > >> On Wed, 30 Jun 2004, Sourangshu Bhattacharya wrote: >> >> >> >>> Hi, >>> >>> Is there a direct way (without reading the protein name from >>> swissprot and searching in PDB) of getting the PDB id of the protein >>> corresponding to a particular Swissprot id ? >>> >> >> >> I would use the MSD database, which maintains a manually curated version >> of the SwissProt to PDB mapping. >> >> >> >>> Also, how do I know whether structure for a particular protein >>> corresponding to a swissprot id has been determined or not ? >>> >> >> >> Strictly speeking, the above mapping gives you this. More realistically, >> however, you can consider very close homologues to the above set as also >> 'solved'. Where you draw the line is a matter of requirement, but you can >> get reasonable models (allegedly) at > 40% sequence identity, or >> reasonable 'fold prediction' at much larger distances (see SUPERFAMILY >> for >> example). >> >> It all depends on what you want to do. >> >> >> >>> Thank you very much.. >>> >>> Regards, >>> Sourangshu. >>> >>> >>> >> >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9930 http://ffas.ljcrf.edu/~iddo From pmr at ebi.ac.uk Thu Jul 1 12:26:49 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Thu, 01 Jul 2004 17:26:49 +0100 Subject: [BiO BB] Getting PDB id from Swissprot entry In-Reply-To: <40E436D7.6060201@csa.iisc.ernet.in> References: <40E2A745.6030400@csa.iisc.ernet.in> <40E4031D.8060108@ebi.ac.uk> <40E436D7.6060201@csa.iisc.ernet.in> Message-ID: <40E43B49.8080509@ebi.ac.uk> Sourangshu Bhattacharya wrote: > Hi Peter, > Actually I am not working with the Swissprot database files, but only > with the web interface. Hmmm ... but still, if you have a web interface to SwissProt you must be able to get to the DR lines somehow ... which web interface? Examples below use AMIC_PSEAE as the SwissProt ID. You can get the full text entry, for example, from the EBI's SRS server as the "pretty" view where "Database cross-references" appear lower down: http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[SWISSPROT:'AMIC_PSEAE'] or as the original text entry with DR lines. http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+EntryPage+-e+[SWISSPROT:AMIC_PSEAE]+-vn+2 If you have EMBOSS installed, you can define remote access through the EBI server, and use "entret" to see the full text entry. There are, of course, many other ways. The Expasy server also gives you the cross references: http://ca.expasy.org/cgi-bin/niceprot.pl?AMIC_PSEAE Hope that helps, Peter Rice, From sourangshu at csa.iisc.ernet.in Thu Jul 1 14:02:26 2004 From: sourangshu at csa.iisc.ernet.in (Sourangshu Bhattacharya) Date: Thu, 01 Jul 2004 23:32:26 +0530 Subject: [BiO BB] Getting PDB id from Swissprot entry In-Reply-To: <40E43899.7030103@burnham.org> References: <40E435B6.5020507@csa.iisc.ernet.in> <40E43899.7030103@burnham.org> Message-ID: <40E451B2.10008@csa.iisc.ernet.in> Hi Iddo, I was going through a paper which gave Swissprot references for some proteins pairs which have circular permutations. I wanted to have a look at their structures. It seems I am facing many of the bellow mentioned problems. Many a times I dont find one of the structures (even homologies). Also, it seems Swissprot lists multiple chains (if present) in some order in one and in another order in the other which is detected as permutations. Unfortunately it is difficult to detect the same with structure alignment within a chain. Thank you very much for the info. It will help me a lot. Regards, Sourangshu. Iddo Friedberg wrote: > Hi, > > I do not know for which particular purpose you are looking for SP <--> > PDB mappings, but beware the following perils & pitfalls: > > 1) The SP <--> PDB mapping can be many-to-many. > > 1.1 )There may be several entries in PDB which correspond to a single > swissprot entry. This is because the same protein may have been > structurally solved by different groups at different times, solved > with different ligands, point mutated, and so forth. Be very careful > about point-mutations: they do not have the same sequence in PDB as in > SP. > > 1.2) At the same time, there may be several SP entries corresponding > to a single PDB entry. This may be due to SP redundancy (although > database curators are doing a fantastic job of keeping that down), > close homologs, or point mutations. > > 2) An SP amino-acid sequence is rarely the same as the PDB sequence. > Usually only part of a structure is solved. Gaps abound, because > crystallographers sometimes cannot see the loops. There are large > deletions, because there are bits which are not crystallizable, or, if > NMR, they are trying to keep the protein short. > > 3) There are many SP entries which do have an equivalent in PDB, but > it does not say so in DR or PDB. See also the "40%" comment below. > > Cheers, > > Iddo > > > > Sourangshu Bhattacharya wrote: > >> Hi Dan, >> Thank you very much. I didn't know about MSD. >> >> There is also an entry HSSP in swissprot which gives homologues. >> >> Sourangshu >> >> Dan Bolser wrote: >> >>> On Wed, 30 Jun 2004, Sourangshu Bhattacharya wrote: >>> >>> >>> >>>> Hi, >>>> >>>> Is there a direct way (without reading the protein name from >>>> swissprot and searching in PDB) of getting the PDB id of the >>>> protein corresponding to a particular Swissprot id ? >>>> >>> >>> >>> >>> I would use the MSD database, which maintains a manually curated >>> version >>> of the SwissProt to PDB mapping. >>> >>> >>> >>>> Also, how do I know whether structure for a particular protein >>>> corresponding to a swissprot id has been determined or not ? >>>> >>> >>> >>> >>> Strictly speeking, the above mapping gives you this. More >>> realistically, >>> however, you can consider very close homologues to the above set as >>> also >>> 'solved'. Where you draw the line is a matter of requirement, but >>> you can >>> get reasonable models (allegedly) at > 40% sequence identity, or >>> reasonable 'fold prediction' at much larger distances (see >>> SUPERFAMILY for >>> example). >>> >>> It all depends on what you want to do. >>> >>> >>> >>>> Thank you very much.. >>>> >>>> Regards, >>>> Sourangshu. >>>> >>>> >>>> >>> >>> >>> >>> _______________________________________________ >>> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >>> >>> >> > -- Sourangshu Bhattacharya PhD Student, Dept. of Computer Science & Automation, Indian Institute of Science, Bangalore - 560012, India. Website: http://people.csa.iisc.ernet.in/sourangshu Cell Phone : 91-98457 97492 From idoerg at burnham.org Thu Jul 1 14:15:07 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Thu, 01 Jul 2004 11:15:07 -0700 Subject: [BiO BB] Getting PDB id from Swissprot entry In-Reply-To: <40E451B2.10008@csa.iisc.ernet.in> References: <40E435B6.5020507@csa.iisc.ernet.in> <40E43899.7030103@burnham.org> <40E451B2.10008@csa.iisc.ernet.in> Message-ID: <40E454AB.6040307@burnham.org> The best thing for you to do would be to BLAST the SP sequence against PDB, and take the top hit. HTH, ./I Sourangshu Bhattacharya wrote: > Hi Iddo, > > I was going through a paper which gave Swissprot references for some > proteins pairs which have circular permutations. > I wanted to have a look at their structures. > > It seems I am facing many of the bellow mentioned problems. Many a times > I dont find one of the structures (even homologies). > Also, it seems Swissprot lists multiple chains (if present) in some > order in one and in another order in the other which is detected as > permutations. > Unfortunately it is difficult to detect the same with structure > alignment within a chain. > > Thank you very much for the info. It will help me a lot. > Regards, > Sourangshu. > > Iddo Friedberg wrote: > >> Hi, >> >> I do not know for which particular purpose you are looking for SP <--> >> PDB mappings, but beware the following perils & pitfalls: >> >> 1) The SP <--> PDB mapping can be many-to-many. >> >> 1.1 )There may be several entries in PDB which correspond to a single >> swissprot entry. This is because the same protein may have been >> structurally solved by different groups at different times, solved >> with different ligands, point mutated, and so forth. Be very careful >> about point-mutations: they do not have the same sequence in PDB as in >> SP. >> >> 1.2) At the same time, there may be several SP entries corresponding >> to a single PDB entry. This may be due to SP redundancy (although >> database curators are doing a fantastic job of keeping that down), >> close homologs, or point mutations. >> >> 2) An SP amino-acid sequence is rarely the same as the PDB sequence. >> Usually only part of a structure is solved. Gaps abound, because >> crystallographers sometimes cannot see the loops. There are large >> deletions, because there are bits which are not crystallizable, or, if >> NMR, they are trying to keep the protein short. >> >> 3) There are many SP entries which do have an equivalent in PDB, but >> it does not say so in DR or PDB. See also the "40%" comment below. >> >> Cheers, >> >> Iddo >> >> >> >> Sourangshu Bhattacharya wrote: >> >>> Hi Dan, >>> Thank you very much. I didn't know about MSD. >>> >>> There is also an entry HSSP in swissprot which gives homologues. >>> >>> Sourangshu >>> >>> Dan Bolser wrote: >>> >>>> On Wed, 30 Jun 2004, Sourangshu Bhattacharya wrote: >>>> >>>> >>>> >>>>> Hi, >>>>> >>>>> Is there a direct way (without reading the protein name from >>>>> swissprot and searching in PDB) of getting the PDB id of the >>>>> protein corresponding to a particular Swissprot id ? >>>>> >>>> >>>> >>>> >>>> >>>> I would use the MSD database, which maintains a manually curated >>>> version >>>> of the SwissProt to PDB mapping. >>>> >>>> >>>> >>>>> Also, how do I know whether structure for a particular protein >>>>> corresponding to a swissprot id has been determined or not ? >>>>> >>>> >>>> >>>> >>>> >>>> Strictly speeking, the above mapping gives you this. More >>>> realistically, >>>> however, you can consider very close homologues to the above set as >>>> also >>>> 'solved'. Where you draw the line is a matter of requirement, but >>>> you can >>>> get reasonable models (allegedly) at > 40% sequence identity, or >>>> reasonable 'fold prediction' at much larger distances (see >>>> SUPERFAMILY for >>>> example). >>>> >>>> It all depends on what you want to do. >>>> >>>> >>>> >>>>> Thank you very much.. >>>>> >>>>> Regards, >>>>> Sourangshu. >>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >>>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >>>> >>>> >>> >> > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9930 http://ffas.ljcrf.edu/~iddo From dmnunif at charter.net Thu Jul 1 22:46:09 2004 From: dmnunif at charter.net (D. Norris) Date: Thu, 1 Jul 2004 21:46:09 -0500 Subject: [BiO BB] Getting PDB id from Swissprot entry References: <40E2A745.6030400@csa.iisc.ernet.in> Message-ID: <000d01c45fde$baf31dd0$1976b118@VALUED4DA88152> Hi: Our bioinformatics is on the electrochemistry of how proteins transduce abiotic energy into info in actual biological systems- i.e., live cells and multi-cellular organisms dmn ----- Original Message ----- From: "Sourangshu Bhattacharya" To: Sent: Wednesday, June 30, 2004 6:43 AM Subject: [BiO BB] Getting PDB id from Swissprot entry > Hi, > > Is there a direct way (without reading the protein name from swissprot > and searching in PDB) of getting the PDB id of the protein corresponding > to a particular Swissprot id ? > > Also, how do I know whether structure for a particular protein > corresponding to a swissprot id has been determined or not ? > > Thank you very much.. > > Regards, > Sourangshu. > > -- > > Sourangshu Bhattacharya > PhD Student, > Dept. of Computer Science & Automation, > Indian Institute of Science, > Bangalore - 560012, India. > > Website: http://people.csa.iisc.ernet.in/sourangshu > Cell Phone : 91-98457 97492 > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From dmnunif at charter.net Thu Jul 1 22:51:01 2004 From: dmnunif at charter.net (D. Norris) Date: Thu, 1 Jul 2004 21:51:01 -0500 Subject: [BiO BB] Getting PDB id from Swissprot entry References: Message-ID: <001301c45fdf$68e96b10$1976b118@VALUED4DA88152> Hi: Meaningful bioinformatics must work in the whole cell, and whole multicellular organism. Genomics and proteomics alone are just lists of parts--no more, no less !!! dmn ----- Original Message ----- From: "Dan Bolser" To: Cc: Sent: Wednesday, June 30, 2004 8:32 AM Subject: Re: [BiO BB] Getting PDB id from Swissprot entry > On Wed, 30 Jun 2004, Sourangshu Bhattacharya wrote: > > >Hi, > > > >Is there a direct way (without reading the protein name from swissprot > >and searching in PDB) of getting the PDB id of the protein corresponding > >to a particular Swissprot id ? > > I would use the MSD database, which maintains a manually curated version > of the SwissProt to PDB mapping. > > >Also, how do I know whether structure for a particular protein > >corresponding to a swissprot id has been determined or not ? > > Strictly speeking, the above mapping gives you this. More realistically, > however, you can consider very close homologues to the above set as also > 'solved'. Where you draw the line is a matter of requirement, but you can > get reasonable models (allegedly) at > 40% sequence identity, or > reasonable 'fold prediction' at much larger distances (see SUPERFAMILY for > example). > > It all depends on what you want to do. > > >Thank you very much.. > > > >Regards, > >Sourangshu. > > > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From dmnunif at charter.net Thu Jul 1 22:52:08 2004 From: dmnunif at charter.net (D. Norris) Date: Thu, 1 Jul 2004 21:52:08 -0500 Subject: [BiO BB] Mandrake 10.0 and Swiss PDB viewer References: <40E3030A.9040301@burnham.org> Message-ID: <001901c45fdf$90f7c840$1976b118@VALUED4DA88152> No way, Jose dmn ----- Original Message ----- From: "Iddo Friedberg" To: Sent: Wednesday, June 30, 2004 1:14 PM Subject: [BiO BB] Mandrake 10.0 and Swiss PDB viewer > Hi all, > > I recently installed Mandrake 10.0, and I an trying to run > SwissPDB-Viewer, which worked fine on my RH7.3 machine. > > When I run the lates version (3.7sp5) I get a: > > /usr/share/SPDBV/bin/spdbv.Linux: error while loading shared libraries: > libXm.so.3: cannot open shared object file: No such file or directory > > A symolic link: > /usr/X11R6/lib/libXm.so.3 -> /usr/X11R6/lib/libXm.so.2.0.1 > > and /sbin/ldconfig > did not help. > > Downgrading to version 3.7 I manage to run the program, but I get no > test in the menu bar area, rendering spdbv pretty much useless. Changing > color depth on the graphics device did not help. > > Help? > > Thanks, > > Iddo > > > -- > Iddo Friedberg, Ph.D. > The Burnham Institute > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037 USA > Tel: +1 (858) 646 3100 x3516 > Fax: +1 (858) 713 9930 > http://ffas.ljcrf.edu/~iddo > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From dmnunif at charter.net Thu Jul 1 22:58:05 2004 From: dmnunif at charter.net (D. Norris) Date: Thu, 1 Jul 2004 21:58:05 -0500 Subject: [BiO BB] Getting PDB id from Swissprot entry References: <40E435B6.5020507@csa.iisc.ernet.in> <40E43899.7030103@burnham.org> <40E451B2.10008@csa.iisc.ernet.in> <40E454AB.6040307@burnham.org> Message-ID: <002d01c45fe0$6606c810$1976b118@VALUED4DA88152> You will never really contribute much until you remember that a biological system far exceeds lists of genes and proteins, i.e., parts lists. dmn ----- Original Message ----- From: "Iddo Friedberg" To: Sent: Thursday, July 01, 2004 1:15 PM Subject: Re: [BiO BB] Getting PDB id from Swissprot entry > > > The best thing for you to do would be to BLAST the SP sequence against > PDB, and take the top hit. > > HTH, > > ./I > > Sourangshu Bhattacharya wrote: > > Hi Iddo, > > > > I was going through a paper which gave Swissprot references for some > > proteins pairs which have circular permutations. > > I wanted to have a look at their structures. > > > > It seems I am facing many of the bellow mentioned problems. Many a times > > I dont find one of the structures (even homologies). > > Also, it seems Swissprot lists multiple chains (if present) in some > > order in one and in another order in the other which is detected as > > permutations. > > Unfortunately it is difficult to detect the same with structure > > alignment within a chain. > > > > Thank you very much for the info. It will help me a lot. > > Regards, > > Sourangshu. > > > > Iddo Friedberg wrote: > > > >> Hi, > >> > >> I do not know for which particular purpose you are looking for SP <--> > >> PDB mappings, but beware the following perils & pitfalls: > >> > >> 1) The SP <--> PDB mapping can be many-to-many. > >> > >> 1.1 )There may be several entries in PDB which correspond to a single > >> swissprot entry. This is because the same protein may have been > >> structurally solved by different groups at different times, solved > >> with different ligands, point mutated, and so forth. Be very careful > >> about point-mutations: they do not have the same sequence in PDB as in > >> SP. > >> > >> 1.2) At the same time, there may be several SP entries corresponding > >> to a single PDB entry. This may be due to SP redundancy (although > >> database curators are doing a fantastic job of keeping that down), > >> close homologs, or point mutations. > >> > >> 2) An SP amino-acid sequence is rarely the same as the PDB sequence. > >> Usually only part of a structure is solved. Gaps abound, because > >> crystallographers sometimes cannot see the loops. There are large > >> deletions, because there are bits which are not crystallizable, or, if > >> NMR, they are trying to keep the protein short. > >> > >> 3) There are many SP entries which do have an equivalent in PDB, but > >> it does not say so in DR or PDB. See also the "40%" comment below. > >> > >> Cheers, > >> > >> Iddo > >> > >> > >> > >> Sourangshu Bhattacharya wrote: > >> > >>> Hi Dan, > >>> Thank you very much. I didn't know about MSD. > >>> > >>> There is also an entry HSSP in swissprot which gives homologues. > >>> > >>> Sourangshu > >>> > >>> Dan Bolser wrote: > >>> > >>>> On Wed, 30 Jun 2004, Sourangshu Bhattacharya wrote: > >>>> > >>>> > >>>> > >>>>> Hi, > >>>>> > >>>>> Is there a direct way (without reading the protein name from > >>>>> swissprot and searching in PDB) of getting the PDB id of the > >>>>> protein corresponding to a particular Swissprot id ? > >>>>> > >>>> > >>>> > >>>> > >>>> > >>>> I would use the MSD database, which maintains a manually curated > >>>> version > >>>> of the SwissProt to PDB mapping. > >>>> > >>>> > >>>> > >>>>> Also, how do I know whether structure for a particular protein > >>>>> corresponding to a swissprot id has been determined or not ? > >>>>> > >>>> > >>>> > >>>> > >>>> > >>>> Strictly speeking, the above mapping gives you this. More > >>>> realistically, > >>>> however, you can consider very close homologues to the above set as > >>>> also > >>>> 'solved'. Where you draw the line is a matter of requirement, but > >>>> you can > >>>> get reasonable models (allegedly) at > 40% sequence identity, or > >>>> reasonable 'fold prediction' at much larger distances (see > >>>> SUPERFAMILY for > >>>> example). > >>>> > >>>> It all depends on what you want to do. > >>>> > >>>> > >>>> > >>>>> Thank you very much.. > >>>>> > >>>>> Regards, > >>>>> Sourangshu. > >>>>> > >>>>> > >>>>> > >>>> > >>>> > >>>> > >>>> > >>>> _______________________________________________ > >>>> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > >>>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > >>>> > >>>> > >>> > >> > > > > -- > Iddo Friedberg, Ph.D. > The Burnham Institute > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037 USA > Tel: +1 (858) 646 3100 x3516 > Fax: +1 (858) 713 9930 > http://ffas.ljcrf.edu/~iddo > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From landman at scalableinformatics.com Thu Jul 1 23:01:31 2004 From: landman at scalableinformatics.com (Joe Landman) Date: Thu, 01 Jul 2004 23:01:31 -0400 Subject: [BiO BB] Mandrake 10.0 and Swiss PDB viewer In-Reply-To: <40E3030A.9040301@burnham.org> References: <40E3030A.9040301@burnham.org> Message-ID: <1088737290.15669.114.camel@protein.scalableinformatics.com> Hi Iddo: Some folks link against lesstif, some link against OpenMotif. According to the RPM db crunch:~ # rpm -qf /usr/X11R6/lib/libXm.so.3 openmotif-libs-2.2.2-355 You can find openmotif at http://www.opengroup.org/openmotif/ or at http://rpmfind.net/linux/rpm2html/search.php?query=openmotif or http://rpm.pbone.net/index.php3?stat=3&search=openmotif&srodzaj=4&dl=80&sourceid=Mozilla-search Joe On Wed, 2004-06-30 at 14:14, Iddo Friedberg wrote: > Hi all, > > I recently installed Mandrake 10.0, and I an trying to run > SwissPDB-Viewer, which worked fine on my RH7.3 machine. > > When I run the lates version (3.7sp5) I get a: > > /usr/share/SPDBV/bin/spdbv.Linux: error while loading shared libraries: > libXm.so.3: cannot open shared object file: No such file or directory > > A symolic link: > /usr/X11R6/lib/libXm.so.3 -> /usr/X11R6/lib/libXm.so.2.0.1 > > and /sbin/ldconfig > did not help. > > Downgrading to version 3.7 I manage to run the program, but I get no > test in the menu bar area, rendering spdbv pretty much useless. Changing > color depth on the graphics device did not help. > > Help? > > Thanks, > > Iddo -- Joseph Landman, Ph.D Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://scalableinformatics.com phone: +1 734 612 4615 From ekeen at mail.tongji.edu.cn Fri Jul 2 00:22:35 2004 From: ekeen at mail.tongji.edu.cn (ekeen) Date: Fri, 2 Jul 2004 12:22:35 +0800 Subject: [BiO BB] The third circular of the International Conference on Chemometrics and Bioinformatics in Asia 2004 In-Reply-To: <001301c45fdf$68e96b10$1976b118@VALUED4DA88152> Message-ID: <20040702044221.ACDA51087D1@mail.tongji.edu.cn> Dear Colleagues: We would like to invite you to contribute to the International Conference on Chemometrics and Bioinformatics in Asia 2004 (CCBA-2004) here find you the third circular of CCBA-2004. In this conference, the following specific topics will be included: Quantitative Structure and Activity Relationship in Chemistry and Medicines Bioinformatics for Microarrays in Medicines and Pharmacology Data Mining in Chemistry and Medicine Near-Infrared Spectroscopy and Chemometrics Multivariate Calibration and Resolution Experimental Design and Process Chemometrics Combining Hard and Soft Models for Data Mining Image Analysis in Chemistry and Medicine Multiway and Multiblock Issues Support Vector Machines and Neural Nets in Chemistry and Medicine Classification and Pattern Detection and Recognition Please let us know if you have paper(s) that you would like to contribute, or if you know of colleagues that may like to submit their works to these special sessions. SUBMISSION OF ABSTRACTS: Abstracts submitted for presentation in the CCBA2004 conference should be sent to the address of cheminfo at tongji.edu.cn in WORD 97 or 2000 format. In the e-mail, authors should attach an abstract submission form for each submitted paper to provide the following details: 1. Mini-symposium(s) or Topic(s). 2. Preferred presentation. (Oral/Poster) 3. Name(s) of author(s). Indicate by underline the presenting author and an asterisk (*) for the corresponding author. Family names for all authors should be in capital letters. 4. The institution(s) of the author(s). 5. The address of the corresponding author. 6. TEL and FAX number. 7. The corresponding E-mail address of the corresponding author. 8. Title in capital letters. 9. An abstract within 200 words in English must be attached. IMPORTANT DATES: Jun. 30, 2004 Submission of abstracts for oral and poster presentation. (Still open for new registers) Jul. 20, 2004 Notification of acceptance and form of presentation of contributions. Jul. 30, 2004 Early registration period ends. Jul. 30, 2004 Deadline for payment of the early registration fee Oct. 16, 2004 Submission of manuscripts for publication in Proceedings at the conference registration desk. Best wishes, Tonghua Li and Kai Chen Molecular Science Laboratory Department of Chemistry Tongji University Shanghai, 200092 P. R. China Tel.: (86) 21-6598-3987 (office) FAX: (86) 21-6598-3987-8004 WebSite: http://cheminfo.tongji.edu.cn/ccba2004/ From dmb at mrc-dunn.cam.ac.uk Fri Jul 2 04:57:58 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 2 Jul 2004 09:57:58 +0100 (BST) Subject: [BiO BB] Getting PDB id from Swissprot entry In-Reply-To: <001301c45fdf$68e96b10$1976b118@VALUED4DA88152> Message-ID: On Thu, 1 Jul 2004, D. Norris wrote: >Hi: > >Meaningful bioinformatics must work in the whole cell, and whole >multicellular organism. Genomics and proteomics alone are just lists of >parts--no more, no less !!! I agree, but can you suggest a 'whole cell' or 'organism' framework that I can use? dan > >dmn >----- Original Message ----- >From: "Dan Bolser" >To: >Cc: >Sent: Wednesday, June 30, 2004 8:32 AM >Subject: Re: [BiO BB] Getting PDB id from Swissprot entry > > >> On Wed, 30 Jun 2004, Sourangshu Bhattacharya wrote: >> >> >Hi, >> > >> >Is there a direct way (without reading the protein name from swissprot >> >and searching in PDB) of getting the PDB id of the protein corresponding >> >to a particular Swissprot id ? >> >> I would use the MSD database, which maintains a manually curated version >> of the SwissProt to PDB mapping. >> >> >Also, how do I know whether structure for a particular protein >> >corresponding to a swissprot id has been determined or not ? >> >> Strictly speeking, the above mapping gives you this. More realistically, >> however, you can consider very close homologues to the above set as also >> 'solved'. Where you draw the line is a matter of requirement, but you can >> get reasonable models (allegedly) at > 40% sequence identity, or >> reasonable 'fold prediction' at much larger distances (see SUPERFAMILY for >> example). >> >> It all depends on what you want to do. >> >> >Thank you very much.. >> > >> >Regards, >> >Sourangshu. >> > >> > >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From nchandra at physics.iisc.ernet.in Fri Jul 2 05:07:40 2004 From: nchandra at physics.iisc.ernet.in (Dr.Nagasuma Chandra) Date: Fri, 2 Jul 2004 14:37:40 +0530 (IST) Subject: [BiO BB] Getting PDB id from Swissprot entry In-Reply-To: Message-ID: I agree too and would ask the same question that Dan asked, but dont see the relevance of this thread to the specific question Sourangshu asked. Sourangshu, if you are looking for the exact match, then fetching the DR lines is the simplest, but what Iddo said still holds good (of many-many matches in some cases, part domain/missing loops in some cases)- all depends on what you are looking for. Nagasuma Chandra *********************************************** Dr. Nagasuma Chandra Bioinformatics centre Indian Institute of Science Bangalore 560 012 Tel: +91-80-22932469 or 23601409 Fax: +91-80-23600551 e-mail: nchandra at physics.iisc.ernet.in *********************************************** On Fri, 2 Jul 2004, Dan Bolser wrote: > On Thu, 1 Jul 2004, D. Norris wrote: > > >Hi: > > > >Meaningful bioinformatics must work in the whole cell, and whole > >multicellular organism. Genomics and proteomics alone are just lists of > >parts--no more, no less !!! > > I agree, but can you suggest a 'whole cell' or 'organism' framework that I > can use? > > dan > > > > >dmn > >----- Original Message ----- > >From: "Dan Bolser" > >To: > >Cc: > >Sent: Wednesday, June 30, 2004 8:32 AM > >Subject: Re: [BiO BB] Getting PDB id from Swissprot entry > > > > > >> On Wed, 30 Jun 2004, Sourangshu Bhattacharya wrote: > >> > >> >Hi, > >> > > >> >Is there a direct way (without reading the protein name from swissprot > >> >and searching in PDB) of getting the PDB id of the protein corresponding > >> >to a particular Swissprot id ? > >> > >> I would use the MSD database, which maintains a manually curated version > >> of the SwissProt to PDB mapping. > >> > >> >Also, how do I know whether structure for a particular protein > >> >corresponding to a swissprot id has been determined or not ? > >> > >> Strictly speeking, the above mapping gives you this. More realistically, > >> however, you can consider very close homologues to the above set as also > >> 'solved'. Where you draw the line is a matter of requirement, but you can > >> get reasonable models (allegedly) at > 40% sequence identity, or > >> reasonable 'fold prediction' at much larger distances (see SUPERFAMILY for > >> example). > >> > >> It all depends on what you want to do. > >> > >> >Thank you very much.. > >> > > >> >Regards, > >> >Sourangshu. > >> > > >> > > >> > >> _______________________________________________ > >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > >_______________________________________________ > >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From idoerg at burnham.org Fri Jul 2 12:15:29 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Fri, 02 Jul 2004 09:15:29 -0700 Subject: [Biodevelopers] Re: [BiO BB] Mandrake 10.0 and Swiss PDB viewer In-Reply-To: <1088737290.15669.114.camel@protein.scalableinformatics.com> References: <40E3030A.9040301@burnham.org> <1088737290.15669.114.camel@protein.scalableinformatics.com> Message-ID: <40E58A21.6090307@burnham.org> openmotif-2.2.3 with spdbv 3.7sp5 did the trick. Thanks Joe! ./I Joe Landman wrote: > Hi Iddo: > > Some folks link against lesstif, some link against OpenMotif. > According to the RPM db > > crunch:~ # rpm -qf /usr/X11R6/lib/libXm.so.3 > openmotif-libs-2.2.2-355 > > You can find openmotif at http://www.opengroup.org/openmotif/ or at > http://rpmfind.net/linux/rpm2html/search.php?query=openmotif or > http://rpm.pbone.net/index.php3?stat=3&search=openmotif&srodzaj=4&dl=80&sourceid=Mozilla-search > > Joe > > On Wed, 2004-06-30 at 14:14, Iddo Friedberg wrote: > >>Hi all, >> >>I recently installed Mandrake 10.0, and I an trying to run >>SwissPDB-Viewer, which worked fine on my RH7.3 machine. >> >>When I run the lates version (3.7sp5) I get a: >> >>/usr/share/SPDBV/bin/spdbv.Linux: error while loading shared libraries: >>libXm.so.3: cannot open shared object file: No such file or directory >> >>A symolic link: >>/usr/X11R6/lib/libXm.so.3 -> /usr/X11R6/lib/libXm.so.2.0.1 >> >>and /sbin/ldconfig >>did not help. >> >>Downgrading to version 3.7 I manage to run the program, but I get no >>test in the menu bar area, rendering spdbv pretty much useless. Changing >>color depth on the graphics device did not help. >> >>Help? >> >>Thanks, >> >>Iddo -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9930 http://ffas.ljcrf.edu/~iddo From sourangshu at csa.iisc.ernet.in Fri Jul 2 14:29:17 2004 From: sourangshu at csa.iisc.ernet.in (Sourangshu Bhattacharya) Date: Fri, 02 Jul 2004 23:59:17 +0530 Subject: [BiO BB] Getting PDB id from Swissprot entry In-Reply-To: References: Message-ID: <40E5A97D.3050207@csa.iisc.ernet.in> Madam, Thank you very much for the advice. I also found some more PDB files which are supposed to have permutations. I am going through them. In many cases, I find there is a repeat of domains. Regards, Sourangshu. Dr.Nagasuma Chandra wrote: >I agree too and would ask the same question that Dan asked, but dont see >the relevance of this thread to the specific question Sourangshu asked. > >Sourangshu, if you are looking for the exact match, then fetching the DR >lines is the simplest, but what Iddo said still holds good (of many-many >matches in some cases, part domain/missing loops in some cases)- all >depends on what you are looking for. > >Nagasuma Chandra > >*********************************************** > Dr. Nagasuma Chandra > Bioinformatics centre > Indian Institute of Science > Bangalore 560 012 > Tel: +91-80-22932469 or 23601409 > Fax: +91-80-23600551 > e-mail: nchandra at physics.iisc.ernet.in >*********************************************** > > >On Fri, 2 Jul >2004, Dan Bolser wrote: > > > >>On Thu, 1 Jul 2004, D. Norris wrote: >> >> >> >>>Hi: >>> >>>Meaningful bioinformatics must work in the whole cell, and whole >>>multicellular organism. Genomics and proteomics alone are just lists of >>>parts--no more, no less !!! >>> >>> >>I agree, but can you suggest a 'whole cell' or 'organism' framework that I >>can use? >> >>dan >> >> >> >>>dmn >>>----- Original Message ----- >>>From: "Dan Bolser" >>>To: >>>Cc: >>>Sent: Wednesday, June 30, 2004 8:32 AM >>>Subject: Re: [BiO BB] Getting PDB id from Swissprot entry >>> >>> >>> >>> >>>>On Wed, 30 Jun 2004, Sourangshu Bhattacharya wrote: >>>> >>>> >>>> >>>>>Hi, >>>>> >>>>>Is there a direct way (without reading the protein name from swissprot >>>>>and searching in PDB) of getting the PDB id of the protein corresponding >>>>>to a particular Swissprot id ? >>>>> >>>>> >>>>I would use the MSD database, which maintains a manually curated version >>>>of the SwissProt to PDB mapping. >>>> >>>> >>>> >>>>>Also, how do I know whether structure for a particular protein >>>>>corresponding to a swissprot id has been determined or not ? >>>>> >>>>> >>>>Strictly speeking, the above mapping gives you this. More realistically, >>>>however, you can consider very close homologues to the above set as also >>>>'solved'. Where you draw the line is a matter of requirement, but you can >>>>get reasonable models (allegedly) at > 40% sequence identity, or >>>>reasonable 'fold prediction' at much larger distances (see SUPERFAMILY for >>>>example). >>>> >>>>It all depends on what you want to do. >>>> >>>> >>>> >>>>>Thank you very much.. >>>>> >>>>>Regards, >>>>>Sourangshu. >>>>> >>>>> >>>>> >>>>> >>>>_______________________________________________ >>>>BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >>>>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >>>> >>>> >>>_______________________________________________ >>>BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >>>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >>> >>> >>> >>_______________________________________________ >>BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> >> > > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- Sourangshu Bhattacharya PhD Student, Dept. of Computer Science & Automation, Indian Institute of Science, Bangalore - 560012, India. Website: http://people.csa.iisc.ernet.in/sourangshu Cell Phone : 91-98457 97492 From dmnunif at charter.net Sat Jul 3 11:08:41 2004 From: dmnunif at charter.net (D. Norris) Date: Sat, 3 Jul 2004 10:08:41 -0500 Subject: [BiO BB] Getting PDB id from Swissprot entry References: Message-ID: <001701c4610f$a0d93650$1976b118@VALUED4DA88152> Hi Dan: We at Unifinium Ltd., and the University of Wisconsin-Madison, have worked, quite effectively we think, on bioinformatics for about 40 years using whole live insect systems, and about 11 standardized in vitro systems extracted from the whole insect biological system. Data obtained from any of the in vitro systems can be readily translated into the data (i.e., biological information) obtained by any of the other in vitro systems, and into the ultimate behavioral change induced in the whole insect system by the abiotic (affector) messenger (e.g., feeding inhibitor, or kairomone). Our continuing major (central)experimental focus has been on the involved qualitative and quantitative changes in the electrochemistry of proteins. We have had much fun, and believe that we have made very meaningful contributions to bioinformatics. Redox (exchange) chemistry is very central in our findings. Pretinent publications involving Norris, and associates, start in ~ 1969 (Nature) and continue to the present review soon to be published. dmn ----- Original Message ----- From: "Dan Bolser" To: Sent: Friday, July 02, 2004 3:57 AM Subject: Re: [BiO BB] Getting PDB id from Swissprot entry > On Thu, 1 Jul 2004, D. Norris wrote: > > >Hi: > > > >Meaningful bioinformatics must work in the whole cell, and whole > >multicellular organism. Genomics and proteomics alone are just lists of > >parts--no more, no less !!! > > I agree, but can you suggest a 'whole cell' or 'organism' framework that I > can use? > > dan > > > > >dmn > >----- Original Message ----- > >From: "Dan Bolser" > >To: > >Cc: > >Sent: Wednesday, June 30, 2004 8:32 AM > >Subject: Re: [BiO BB] Getting PDB id from Swissprot entry > > > > > >> On Wed, 30 Jun 2004, Sourangshu Bhattacharya wrote: > >> > >> >Hi, > >> > > >> >Is there a direct way (without reading the protein name from swissprot > >> >and searching in PDB) of getting the PDB id of the protein corresponding > >> >to a particular Swissprot id ? > >> > >> I would use the MSD database, which maintains a manually curated version > >> of the SwissProt to PDB mapping. > >> > >> >Also, how do I know whether structure for a particular protein > >> >corresponding to a swissprot id has been determined or not ? > >> > >> Strictly speeking, the above mapping gives you this. More realistically, > >> however, you can consider very close homologues to the above set as also > >> 'solved'. Where you draw the line is a matter of requirement, but you can > >> get reasonable models (allegedly) at > 40% sequence identity, or > >> reasonable 'fold prediction' at much larger distances (see SUPERFAMILY for > >> example). > >> > >> It all depends on what you want to do. > >> > >> >Thank you very much.. > >> > > >> >Regards, > >> >Sourangshu. > >> > > >> > > >> > >> _______________________________________________ > >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > >_______________________________________________ > >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From dmnunif at charter.net Sat Jul 3 11:14:58 2004 From: dmnunif at charter.net (D. Norris) Date: Sat, 3 Jul 2004 10:14:58 -0500 Subject: [BiO BB] Getting PDB id from Swissprot entry References: Message-ID: <001d01c46110$816fdf20$1976b118@VALUED4DA88152> Dr. Chandra: If Sourangshu's question is really relevant to bioinformatics in a whole biological system, then dmn thinks there must be some relevance to our thread.. dmn ----- Original Message ----- From: "Dr.Nagasuma Chandra" To: Sent: Friday, July 02, 2004 4:07 AM Subject: Re: [BiO BB] Getting PDB id from Swissprot entry > > I agree too and would ask the same question that Dan asked, but dont see > the relevance of this thread to the specific question Sourangshu asked. > > Sourangshu, if you are looking for the exact match, then fetching the DR > lines is the simplest, but what Iddo said still holds good (of many-many > matches in some cases, part domain/missing loops in some cases)- all > depends on what you are looking for. > > Nagasuma Chandra > > *********************************************** > Dr. Nagasuma Chandra > Bioinformatics centre > Indian Institute of Science > Bangalore 560 012 > Tel: +91-80-22932469 or 23601409 > Fax: +91-80-23600551 > e-mail: nchandra at physics.iisc.ernet.in > *********************************************** > > > On Fri, 2 Jul > 2004, Dan Bolser wrote: > > > On Thu, 1 Jul 2004, D. Norris wrote: > > > > >Hi: > > > > > >Meaningful bioinformatics must work in the whole cell, and whole > > >multicellular organism. Genomics and proteomics alone are just lists of > > >parts--no more, no less !!! > > > > I agree, but can you suggest a 'whole cell' or 'organism' framework that I > > can use? > > > > dan > > > > > > > >dmn > > >----- Original Message ----- > > >From: "Dan Bolser" > > >To: > > >Cc: > > >Sent: Wednesday, June 30, 2004 8:32 AM > > >Subject: Re: [BiO BB] Getting PDB id from Swissprot entry > > > > > > > > >> On Wed, 30 Jun 2004, Sourangshu Bhattacharya wrote: > > >> > > >> >Hi, > > >> > > > >> >Is there a direct way (without reading the protein name from swissprot > > >> >and searching in PDB) of getting the PDB id of the protein corresponding > > >> >to a particular Swissprot id ? > > >> > > >> I would use the MSD database, which maintains a manually curated version > > >> of the SwissProt to PDB mapping. > > >> > > >> >Also, how do I know whether structure for a particular protein > > >> >corresponding to a swissprot id has been determined or not ? > > >> > > >> Strictly speeking, the above mapping gives you this. More realistically, > > >> however, you can consider very close homologues to the above set as also > > >> 'solved'. Where you draw the line is a matter of requirement, but you can > > >> get reasonable models (allegedly) at > 40% sequence identity, or > > >> reasonable 'fold prediction' at much larger distances (see SUPERFAMILY for > > >> example). > > >> > > >> It all depends on what you want to do. > > >> > > >> >Thank you very much.. > > >> > > > >> >Regards, > > >> >Sourangshu. > > >> > > > >> > > > >> > > >> _______________________________________________ > > >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > > > >_______________________________________________ > > >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From dmb at mrc-dunn.cam.ac.uk Sat Jul 3 12:39:17 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Sat, 3 Jul 2004 17:39:17 +0100 (BST) Subject: [BiO BB] Getting PDB id from Swissprot entry In-Reply-To: <001701c4610f$a0d93650$1976b118@VALUED4DA88152> Message-ID: On Sat, 3 Jul 2004, D. Norris wrote: >Hi Dan: > >We at Unifinium Ltd., and the University of Wisconsin-Madison, have worked, >quite effectively we think, on bioinformatics for about 40 years using whole >live insect systems, and about 11 standardized in vitro systems extracted >from the whole insect biological system. Data obtained from any of the in >vitro systems can be readily translated into the data (i.e., biological >information) obtained by any of the other in vitro systems, and into the >ultimate behavioral change induced in the whole insect system by the abiotic >(affector) messenger (e.g., feeding inhibitor, or kairomone). Our continuing >major (central)experimental focus has been on the involved qualitative and >quantitative changes in the electrochemistry of proteins. We have had much >fun, and believe that we have made very meaningful contributions to >bioinformatics. Redox (exchange) chemistry is very central in our findings. >Pretinent publications involving Norris, and associates, start in ~ 1969 >(Nature) and continue to the present review soon to be published. Sounds very interesting! I found Nature. 1969 Jun 28;222(200):1263-4. Transduction mechanism in olfaction and gustation. Norris DM. Is this one of the citations you are referring to? Could you send a few more key citations so I can understand better? Cheers, Dan. > >dmn > > >----- Original Message ----- >From: "Dan Bolser" >To: >Sent: Friday, July 02, 2004 3:57 AM >Subject: Re: [BiO BB] Getting PDB id from Swissprot entry > > >> On Thu, 1 Jul 2004, D. Norris wrote: >> >> >Hi: >> > >> >Meaningful bioinformatics must work in the whole cell, and whole >> >multicellular organism. Genomics and proteomics alone are just lists of >> >parts--no more, no less !!! >> >> I agree, but can you suggest a 'whole cell' or 'organism' framework that I >> can use? >> >> dan >> >> > >> >dmn >> >----- Original Message ----- >> >From: "Dan Bolser" >> >To: >> >Cc: >> >Sent: Wednesday, June 30, 2004 8:32 AM >> >Subject: Re: [BiO BB] Getting PDB id from Swissprot entry >> > >> > >> >> On Wed, 30 Jun 2004, Sourangshu Bhattacharya wrote: >> >> >> >> >Hi, >> >> > >> >> >Is there a direct way (without reading the protein name from swissprot >> >> >and searching in PDB) of getting the PDB id of the protein >corresponding >> >> >to a particular Swissprot id ? >> >> >> >> I would use the MSD database, which maintains a manually curated >version >> >> of the SwissProt to PDB mapping. >> >> >> >> >Also, how do I know whether structure for a particular protein >> >> >corresponding to a swissprot id has been determined or not ? >> >> >> >> Strictly speeking, the above mapping gives you this. More >realistically, >> >> however, you can consider very close homologues to the above set as >also >> >> 'solved'. Where you draw the line is a matter of requirement, but you >can >> >> get reasonable models (allegedly) at > 40% sequence identity, or >> >> reasonable 'fold prediction' at much larger distances (see SUPERFAMILY >for >> >> example). >> >> >> >> It all depends on what you want to do. >> >> >> >> >Thank you very much.. >> >> > >> >> >Regards, >> >> >Sourangshu. >> >> > >> >> > >> >> >> >> _______________________________________________ >> >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> > >> > >> >_______________________________________________ >> >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> > >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From dmnunif at charter.net Sun Jul 4 00:54:00 2004 From: dmnunif at charter.net (D. Norris) Date: Sat, 3 Jul 2004 23:54:00 -0500 Subject: [BiO BB] Getting PDB id from Swissprot entry References: Message-ID: <001001c46182$ebeeb930$1976b118@VALUED4DA88152> Hi Dan: I shall provide you with a sizeable list of references tomorrow; it is too late now. Oh, heck, here are a few. You could start with: 1) Norris.1985. Bioelectrochemistry and Bioenergetics 14: 449 - 456. 2)Rozental & Norris. 1973 . Nature 244: 370 - 371. 3)Norris, et al. 1970. Science 170: 754 - 755. 4) Norris, et al. 1976. Comp. Biochem. Physiol. 57C: 55 - 59. 5) Norris.1971. Experientia 27: 531 -532. 6) Singer, et al. 1975. Nature 256: 222 - 223. Extensive reviews of our work to the time: Norris, D. M. 1986. Anti-feeding compounds, pp. 97 - 146, in G. Haug and H. Hoffmann (eds.) Chemistry of Plant Protection. 1. Springer-Velag, Berlin. Norris, D. M. (ed). 1981. Perception of Behavioral Chemicals. Elsevier / North-Holland Biomedical Press, Amsterdam. Etc. Etc. Norris, D.M., and I. Markovic.2003. Tritrophic interactions: The inducible defenses of plants, pp: 87 - 109, in O. Koul and G. S. Dhaliwal (eds.). Predators and Parasitoids, Taylor & Francis, London & New York. See you tomorrow. dmn ----- Original Message ----- From: "Dan Bolser" To: Sent: Saturday, July 03, 2004 11:39 AM Subject: Re: [BiO BB] Getting PDB id from Swissprot entry > On Sat, 3 Jul 2004, D. Norris wrote: > > >Hi Dan: > > > >We at Unifinium Ltd., and the University of Wisconsin-Madison, have worked, > >quite effectively we think, on bioinformatics for about 40 years using whole > >live insect systems, and about 11 standardized in vitro systems extracted > >from the whole insect biological system. Data obtained from any of the in > >vitro systems can be readily translated into the data (i.e., biological > >information) obtained by any of the other in vitro systems, and into the > >ultimate behavioral change induced in the whole insect system by the abiotic > >(affector) messenger (e.g., feeding inhibitor, or kairomone). Our continuing > >major (central)experimental focus has been on the involved qualitative and > >quantitative changes in the electrochemistry of proteins. We have had much > >fun, and believe that we have made very meaningful contributions to > >bioinformatics. Redox (exchange) chemistry is very central in our findings. > >Pretinent publications involving Norris, and associates, start in ~ 1969 > >(Nature) and continue to the present review soon to be published. > > Sounds very interesting! > > I found > > Nature. 1969 Jun 28;222(200):1263-4. > Transduction mechanism in olfaction and gustation. > Norris DM. > > Is this one of the citations you are referring to? > > Could you send a few more key citations so I can understand better? > > Cheers, > Dan. > > > > >dmn > > > > > >----- Original Message ----- > >From: "Dan Bolser" > >To: > >Sent: Friday, July 02, 2004 3:57 AM > >Subject: Re: [BiO BB] Getting PDB id from Swissprot entry > > > > > >> On Thu, 1 Jul 2004, D. Norris wrote: > >> > >> >Hi: > >> > > >> >Meaningful bioinformatics must work in the whole cell, and whole > >> >multicellular organism. Genomics and proteomics alone are just lists of > >> >parts--no more, no less !!! > >> > >> I agree, but can you suggest a 'whole cell' or 'organism' framework that I > >> can use? > >> > >> dan > >> > >> > > >> >dmn > >> >----- Original Message ----- > >> >From: "Dan Bolser" > >> >To: > >> >Cc: > >> >Sent: Wednesday, June 30, 2004 8:32 AM > >> >Subject: Re: [BiO BB] Getting PDB id from Swissprot entry > >> > > >> > > >> >> On Wed, 30 Jun 2004, Sourangshu Bhattacharya wrote: > >> >> > >> >> >Hi, > >> >> > > >> >> >Is there a direct way (without reading the protein name from swissprot > >> >> >and searching in PDB) of getting the PDB id of the protein > >corresponding > >> >> >to a particular Swissprot id ? > >> >> > >> >> I would use the MSD database, which maintains a manually curated > >version > >> >> of the SwissProt to PDB mapping. > >> >> > >> >> >Also, how do I know whether structure for a particular protein > >> >> >corresponding to a swissprot id has been determined or not ? > >> >> > >> >> Strictly speeking, the above mapping gives you this. More > >realistically, > >> >> however, you can consider very close homologues to the above set as > >also > >> >> 'solved'. Where you draw the line is a matter of requirement, but you > >can > >> >> get reasonable models (allegedly) at > 40% sequence identity, or > >> >> reasonable 'fold prediction' at much larger distances (see SUPERFAMILY > >for > >> >> example). > >> >> > >> >> It all depends on what you want to do. > >> >> > >> >> >Thank you very much.. > >> >> > > >> >> >Regards, > >> >> >Sourangshu. > >> >> > > >> >> > > >> >> > >> >> _______________________________________________ > >> >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > >> >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > >> > > >> > > >> >_______________________________________________ > >> >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > >> >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > >> > > >> > >> _______________________________________________ > >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > >_______________________________________________ > >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From postmaster at www.lmcs-online.org Mon Jul 5 06:57:18 2004 From: postmaster at www.lmcs-online.org (Logical Methods in CS) Date: Mon, 5 Jul 2004 12:57:18 +0200 Subject: [BiO BB] New Journal Message-ID: <200407051057.i65AvIa32286@www.lmcs-online.org> NEW JOURNAL----NEW JOURNAL----NEW JOURNAL----NEW JOURNAL----NEW JOURNAL -------------------------EXCUSE MULTIPLE COPIES----------------------- L O G I C A L M E T H O D S I N C O M P U T E R S C I E N C E Dear Colleague: We are writing to inform you about a new open-access, online, refereed journal: "Logical Methods in Computer Science". As an open-access publication, the journal will be freely available on the web. This new journal will be devoted to all theoretical and practical topics in computer science related to logic in a broad sense. You can find the homepage at http://www.lmcs-online.org The journal will open to submissions on September 1, 2004. It will be published under the auspices of The International Federation for Computational Logic: http://www.colognet.org/IFCoLog/. The journal will technically be published as an overlay of the Computing Research Repository (CoRR), see http://arxiv.org/archive/cs/intro.html. On the homepage you find a flier and a leaflet containing the basic information about the new journal. We would appreciate your posting and distributing the information, and encouraging potential authors to submit to Logical Methods in Computer Science. You may have heard about the various developments in the past couple of years in regard to the Open Access movement, see, e.g.,: http://www.zim.mpg.de/openaccess-berlin/berlindeclaration.html http://www.plos.org/ http://www.earlham.edu/~peters/fos/overview.htm and the link "Landscape..." at the jornal website. The open-access idea is that knowledge, including scientific knowledge, should be widely and readily available to society, in a stable and long-term form. The Internet and electronic publishing provides an evident means to that end. Not unrelated are concerns arising from the increasingly high prices charged commercially. There are already a few open-access journals in Computer Science, e.g.: http://www.theoryofcomputing.org/ http://www.jair.org/ and http://www.ai.mit.edu/projects/jmlr/. We are convinced that now is the time to start one in our area of logic and computer science. Yours Sincerely, Jiri Adamek, Gordon D. Plotkin, Dana S. Scott and Moshe Y. Vardi From forward at hongyu.org Tue Jul 6 20:37:35 2004 From: forward at hongyu.org (Hongyu Zhang) Date: Tue, 6 Jul 2004 20:37:35 -0400 Subject: [BiO BB] Java BLAST parser Message-ID: <1089160655.40eb45cfc5c32@hongyu.org> Dear all, I am wondering whether anyone here has done some comparison between different Java BLAST parsers, like BioJava (http://www.biojava.org/ ), BatchBLAST (http://www.hip.harvard.edu/informatics/programs/JAVA%20BLAST%20Parser.html ). I've used BioPerl during the past, but recently I have to use Java for a project, so I would appreciate your input on which Java BLAST parsers to use and how their performances are compared to BioPerl. Thanks, -- Hongyu Zhang, Ph.D. Computational biologist Ceres Inc. From yzz100 at psu.edu Wed Jul 7 18:22:51 2004 From: yzz100 at psu.edu (Anne Y. Zhang) Date: Wed, 7 Jul 2004 18:22:51 -0400 Subject: [BiO BB] find proteins in different organisms References: <20040707160109.BE184D1F27@www.bioinformatics.org> Message-ID: <008101c46470$f1345530$b5c3f383@tablet> Given a protein name, and its sequence. How can I found its copies in different organism? Anyone have suggestion? Thanks a lot! Anne From mjmccorm at mtu.edu Wed Jul 7 20:53:12 2004 From: mjmccorm at mtu.edu (Matt McCormick) Date: Wed, 7 Jul 2004 20:53:12 -0400 (EDT) Subject: [BiO BB] find proteins in different organisms In-Reply-To: <008101c46470$f1345530$b5c3f383@tablet> References: <20040707160109.BE184D1F27@www.bioinformatics.org> <008101c46470$f1345530$b5c3f383@tablet> Message-ID: <1753.24.236.179.54.1089247992.squirrel@huskymail.mtu.edu> Go to the NCBI website and do a BLAST search. Use the program blastp for a start. http://www.ncbi.nlm.nih.gov Also read the tutorial there, as it will provide a good introduction. -Matt McCormick > Given a protein name, and its sequence. > How can I found its copies in different > organism? > Anyone have suggestion? > Thanks a lot! > > Anne > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From sourangshu at csa.iisc.ernet.in Thu Jul 8 00:48:39 2004 From: sourangshu at csa.iisc.ernet.in (Sourangshu Bhattacharya) Date: Thu, 08 Jul 2004 10:18:39 +0530 Subject: [BiO BB] find proteins in different organisms In-Reply-To: <008101c46470$f1345530$b5c3f383@tablet> References: <20040707160109.BE184D1F27@www.bioinformatics.org> <008101c46470$f1345530$b5c3f383@tablet> Message-ID: <40ECD227.2080703@csa.iisc.ernet.in> You can try searching the SCOP database for the protein and same protein from the other organisms will usually be in the same family. But you will be searching through proteins whose structures are known. Sourangshu Anne Y. Zhang wrote: >Given a protein name, and its sequence. >How can I found its copies in different >organism? >Anyone have suggestion? >Thanks a lot! > >Anne >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- Sourangshu Bhattacharya PhD Student, Dept. of Computer Science & Automation, Indian Institute of Science, Bangalore - 560012, India. Website: http://people.csa.iisc.ernet.in/sourangshu Cell Phone : 91-98457 97492 From rasmoo143a at yahoo.com Thu Jul 8 07:06:38 2004 From: rasmoo143a at yahoo.com (jain rashmi) Date: Thu, 8 Jul 2004 04:06:38 -0700 (PDT) Subject: [BiO BB] find proteins in different organisms In-Reply-To: <008101c46470$f1345530$b5c3f383@tablet> Message-ID: <20040708110638.12675.qmail@web12007.mail.yahoo.com> Dear Go for the BLAST for entire database from NCBI, U'll get ur desire result. Rashmi Jain --- "Anne Y. Zhang" wrote: > Given a protein name, and its sequence. > How can I found its copies in different > organism? > Anyone have suggestion? > Thanks a lot! > > Anne > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > __________________________________ Do you Yahoo!? New and Improved Yahoo! Mail - 100MB free storage! http://promotions.yahoo.com/new_mail From forward at hongyu.org Thu Jul 8 12:15:33 2004 From: forward at hongyu.org (Hongyu Zhang) Date: Thu, 8 Jul 2004 12:15:33 -0400 Subject: [BiO BB] Re: find proteins in different organisms In-Reply-To: <20040708160117.66B9ED1F4E@www.bioinformatics.org> References: <20040708160117.66B9ED1F4E@www.bioinformatics.org> Message-ID: <1089303333.40ed7325be714@hongyu.org> Try NCBI COG database http://ncbi.nih.gov/COG/ From jrdewet at umich.edu Thu Jul 8 14:38:40 2004 From: jrdewet at umich.edu (Jeffrey R. de Wet) Date: Thu, 8 Jul 2004 14:38:40 -0400 Subject: [BiO BB] Computational biology short courses, August 2004, University of Michigan Message-ID: <001901c4651a$cd2dea70$b1126cc6@DCR6XP21> University of Michigan, Ann Arbor Short Course in Computational Molecular Biology Cancer Bioinformatics August 4-6, 2004 Proteome Informatics August 5-7, 2004 Bioinformatics August 18-20, 2004 Objectives: Challenging intensive courses covering material from our regular graduate courses on computational biology in a format that is accessible to working scientists. Participants will become familiar with the theory and practice of molecular sequence analysis, proteomics, and processing and analyzing cancer biology data. The aim is to provide an appreciation for how and why different analytic approaches are used, their capabilities and their limitations. We emphasize the use of public domain software tools rather than focusing on a specific commercial package. Participants should be familiar with basic molecular biology and mathematics at the level of college calculus, but programming skills or higher-level computer science experience is not required. The courses are targeted to students at the level of a first or second year doctoral candidate and professional scientist in molecular biology or biotechnology. Each 3-day course consists of 6 hours of daily lectures: 3 hrs. in the morning and 3 hrs. in the afternoon. Cancer Bioinformatics: Cancer bioinformatics, biostatistics and data modeling, web tools and data mining Model organisms and cancer networks, cancer systems biology, integrative cancer biology Biomarkers, tissue microarrays, analysis of microarrary data, cancer proteomics Proteome Informatics: Protein isolation and separation methods, proteome concepts Mass spectrometry, peptide mass fingerprinting, protein expression profiling, data analysis Database structures, database searching and search algorithms, de novo sequence analysis Bioinformatics: Statistics, model based data analysis, HMMs, mathematical methods of gene mapping and gene finding Protein models, threading, dynamic programming optimal and suboptimal RNA alignment and folding Information measures, Karlin-Altschul statistics, Sum statistics, gapped BLAST, database searching Multiple sequence alignment, generalized dynamic programming, phylogeny and molecular evolution Supplemental applied scripting and programming sessions will be offered at some of the courses. Please see the web site for updated information. All participants are encouraged to bring a laptop computer (Windows/Intel) for use in the programming sessions. A CD-ROM containing course lecture notes, problem sets, programming exercises, public domain software and reference material will be distributed. Instructors are from the faculty the University of Michigan Bioinformatics Program. (David States, Philip Andrews, Arul Chinnaiyan, Debashish Gosh, Gil Omenn, and David Lubman) joined by Warren Gish (Washington University), David Tabb (Oak Ridge National Laboratory), Curt Wilkerson (Michigan State University), Brett Phinney (Michigan State University), Michael Zuker (Rensselaer Polytechnic Institute) , Michael Becich (University of Pittsburgh), Mark Rubin (Brigham and Women's) Muneesh Tewari (Dana-Farber Cancer Institute). Graduate students from the program will fill in as teaching assistants. For additional information see: http://www.bioinformatics.med.umich.edu/shortcourse2004/index.html Early application is advised, as the number of participants for these courses has to be restricted. From landman at scalableinformatics.com Mon Jul 12 03:08:36 2004 From: landman at scalableinformatics.com (Joe Landman) Date: Mon, 12 Jul 2004 03:08:36 -0400 Subject: [BiO BB] Bioinformatics Benchmark System version 3 release candidate 1 ready Message-ID: <1089616116.27012.135.camel@protein.scalableinformatics.com> Folks: Much delayed as version 2 went through many rewrites, and we did not release early or often. This will be corrected. http://scalableinformatics.com/BBS/ and http://bioinformatics.org/bbs (they are identical) Much is new in version 3. 1) You no longer need to modify program source to setup your benchmark. A simple XML input file will do. 2) A number of examples are included. We need to document the format better, though if you read the format, you will see that it really isn't complex (this is what took so long oddly enough) 3) A bbsv1.xml input deck that replicates the original benchmarks from last year is included. 4) New baseline example tests have been created using HMMer, multiple BLAST runs, and others. Further baseline tests will be added (and suggestions are always welcome). We are looking at a number of codes including ClustalW, and various chemistry and proteomics codes. 5) Output in multiple formats: plain text, csv (comma separated values), and XML. 6) A dryrun option. Does everything but the final execution. Uses a random sleep rather than a run. Much more code, some of it hinting at things to come. Quite scalable: we ran 100 simultaneous tests on a laptop (learning some surprising things about DBM and performance loss in the process). Documentation has been created at least in the form of man pages. More documentation should be available soon, with details of the formats, configuration, and so forth The code is heavily commented. It is GPLed for GPL projects/products. For commercial products which need to be non-GPL and supported efforts, please contact us. Please give it a spin, and send us a note as to how you found it, what else you might like on it, and what tests you would like to see. If you want to contribute an idea for a test, or even better, a test, please send a note. If you want to help out on coding, please send a note as well. Thanks! -- Joseph Landman, Ph.D Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://scalableinformatics.com phone: +1 734 612 4615 From yjzhang at noble.org Fri Jul 9 13:11:21 2004 From: yjzhang at noble.org (Zhang, Yuanji) Date: Fri, 9 Jul 2004 12:11:21 -0500 Subject: [BiO BB] RE: Some questions of alignment (Evgeny Cheremushkin) Message-ID: <6B4878EA887E6C45AAA5AAC4C6017B0E01801AC0@mail-1.noble.org> Dear Evgeny, Last time we talked about alignment of length L given M mispairs. The total possible alignments are C(L, M). Now I am trying to formalize the second question of number of alignments undetectable by blastn with word size = 7 nt. Suppose '0' represents identity, and '1' for one mismatch (total mismatches = M). How many alignments do not have >=7 continuous '0's? Here is an example :000000010000100001000000 (detectable. L = 24, M = 3) and 100000010000100001000000 (undetectable, no 7 or more '0's in a row). From rasa at obj.hopto.org Mon Jul 12 11:37:57 2004 From: rasa at obj.hopto.org (Rasa Gulbinaite) Date: Mon, 12 Jul 2004 18:37:57 +0300 Subject: [BiO BB] SNP flanking sequnces Message-ID: <1089646677.13105.13.camel@rasa.holo.net> Hello, is there any program that does the same as this web application http://sky.bsd.uchicago.edu/SNPSequer.htm? I mean obtaining SNP flanking sequences of given legth. Because sometimes sequences from NCBI SNP database are too short for some purposes. Thank you all for your help. Rasa From kamal010 at hotmail.com Sat Jul 10 01:06:42 2004 From: kamal010 at hotmail.com (kamal) Date: Sat, 10 Jul 2004 09:06:42 +0400 Subject: [BiO BB] information required Message-ID: I would like to know which course is better biotech or bioinformatics i would also like to know whether i can do masters in bioinformatics after doing bachelors degree in biotech please mail -------------- next part -------------- An HTML attachment was scrubbed... URL: From nuraini at cs.usm.my Wed Jul 14 00:15:20 2004 From: nuraini at cs.usm.my (Nur'Aini Abdul Rashid) Date: Wed, 14 Jul 2004 12:15:20 +0800 (Singapore Standard Time) Subject: [BiO BB] Protein Families. Message-ID: <40F4B358.000003.01911@nuraini.cs.usm.my> Hi All, I'm working on clustering algorithms and looking for data to test on... The problem is I don't quite understand how families is define in proteins.. Can someone explain it.. or tell me where I can learn all those basics ex. What are the differences between protein families, superfamilies and domain Thanks Nora. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: IMSTP.gif Type: image/gif Size: 494 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: BackGrnd.jpg Type: image/jpeg Size: 1431 bytes Desc: not available URL: From hustlf at cs.cmu.edu Wed Jul 14 00:22:57 2004 From: hustlf at cs.cmu.edu (Li Fan) Date: Wed, 14 Jul 2004 00:22:57 -0400 Subject: [BiO BB] online clinical SNPs dataset. In-Reply-To: <40F4B358.000003.01911@nuraini.cs.usm.my> References: <40F4B358.000003.01911@nuraini.cs.usm.my> Message-ID: <40F4B521.4030206@cs.cmu.edu> Hello, I am tring to analyze some SNP data using machine learning methods. Is there any online SNP dataset which contain the SNPs over patients? Thanks Fan From virajj at lycos.com Wed Jul 14 01:39:56 2004 From: virajj at lycos.com (vijaya raj) Date: Wed, 14 Jul 2004 00:39:56 -0500 Subject: [BiO BB] information required Message-ID: <20040714053956.CDB85CA06C@ws7-4.us4.outblaze.com> dear kamal both biotech and bioinfo at equaly good and challenging. ur selection should be based on your interest in wet lab and in computers. if you are a very creative guy, who looks for lot of surprises in biology, willing to go out of the conventional laboratory boundaries..then bioinfo is best. with biotech in bachelors, getting in to bioinfo at masters is very much possible in india. but its difficult the otherway. all the best. vijay -- _______________________________________________ Find what you are looking for with the Lycos Yellow Pages http://r.lycos.com/r/yp_emailfooter/http://yellowpages.lycos.com/default.asp?SRC=lycos10 From rouellette at umuc.edu Wed Jul 14 08:21:26 2004 From: rouellette at umuc.edu (Robert Ouellette) Date: Wed, 14 Jul 2004 08:21:26 -0400 Subject: [BiO BB] information required References: Message-ID: <40F52546.64FF7E64@umuc.edu> UMUC offers a master in Bioinformatics online via our Web Tycho system. Please check the syllabi at http://www.umuc.edu/grad/msbt.shtml bob kamal wrote: > I would like to know which course is better biotech or > bioinformatics i would also like to know whether i can do masters in > bioinformatics after doing bachelors degree in biotech please mail -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rouellette.vcf Type: text/x-vcard Size: 278 bytes Desc: Card for Robert Ouellette URL: From brunomiguel at dequim.ist.utl.pt Wed Jul 14 08:50:11 2004 From: brunomiguel at dequim.ist.utl.pt (Bruno Afonso) Date: Wed, 14 Jul 2004 13:50:11 +0100 Subject: [BiO BB] Protein Families. In-Reply-To: <40F4B358.000003.01911@nuraini.cs.usm.my> References: <40F4B358.000003.01911@nuraini.cs.usm.my> Message-ID: <40F52C03.50609@dequim.ist.utl.pt> I believe those are SCOP definitions? Check out the SCOP paper as well as its references and papers referencing SCOP. If you want a quick explanation, you can grab Structural Bioinformatics (Philip Bourne) from wiley and look on the SCOP chapter. BA Nur'Aini Abdul Rashid wrote: > Hi All, > > I'm working on clustering algorithms and looking for data to test on... > The problem is I don't quite understand how families is define in > proteins.. Can someone explain it.. or tell me where I can learn all > those basics ex. > > What are the differences between protein families, superfamilies and domain > > Thanks > > Nora. > > > ____________________________________________________ > /IncrediMail/ - > *Email has finally evolved* - *_Click Here_* > -- Bruno Miguel Afonso Biological Eng. student D.E.Q. @ I.S.T. - Portugal http://dequim.ist.utl.pt/~bruno/ From prem_and at rediffmail.com Wed Jul 14 09:22:24 2004 From: prem_and at rediffmail.com (Achuthan Prem Anand) Date: 14 Jul 2004 13:22:24 -0000 Subject: [BiO BB] Protein Families. Message-ID: <20040714132224.2628.qmail@webmail30.rediffmail.com> An HTML attachment was scrubbed... URL: -------------- next part -------------- Hi Nora Have a look at the following link. You will find the necessary info. http://scop.mrc-lmb.cam.ac.uk/scop/intro.html Regards Prem On Wed, 14 Jul 2004 Nur'Aini Abdul Rashid wrote : >Hi All, > >I'm working on clustering algorithms and looking for data to test on... The >problem is I don't quite understand how families is define in proteins.. Can >someone explain it.. or tell me where I can learn all those basics ex. > >What are the differences between protein families, superfamilies and domain > >Thanks > >Nora. From Austin.Tanney at arragen.com Wed Jul 14 12:11:27 2004 From: Austin.Tanney at arragen.com (Tanney, Austin) Date: Wed, 14 Jul 2004 17:11:27 +0100 Subject: [BiO BB] information required Message-ID: In general I think it would be a much safer bet to do a degree in Biotech and follow it up with a masters in Bioinformatics. This allows you to experience both lab based and computational biology and would leave you in a position where you could choose which you prefer. Austin -----Original Message----- From: Robert Ouellette [mailto:rouellette at umuc.edu] Sent: 14 July 2004 13:21 To: bio_bulletin_board at bioinformatics.org Subject: [SPAM] - Re: [BiO BB] information required - Email has different SMTP TO: and MIME TO: fields in the email addresses UMUC offers a master in Bioinformatics online via our Web Tycho system. Please check the syllabi at http://www.umuc.edu/grad/msbt.shtml bob kamal wrote: I would like to know which course is better biotech or bioinformatics i would also like to know whether i can do masters in bioinformatics after doing bachelors degree in biotech please mail -------------- next part -------------- An HTML attachment was scrubbed... URL: From ehrlich at zib.de Wed Jul 14 03:24:14 2004 From: ehrlich at zib.de (Christian Ehrlich) Date: Wed, 14 Jul 2004 09:24:14 +0200 Subject: [BiO BB] information required In-Reply-To: References: Message-ID: <113691477.20040714092414@zib.de> Saturday, July 10, 2004, 7:06:42 AM, you wrote: hi iam a studen of bioinformatics at the free university berlin. of course i think bioinformatic would be the better choise :) my information status is taht u can do any master want as long as u have finished a degree at a college/university (dont know the difference, germany usually only got universities and degree schools) best reguadrs christian ehrlich k> I would like to know which course is better biotech or bioinformatics k> ? k> i would also like to know whether i can do masters in k> bioinformatics after doing bachelors degree in biotech k> ? k> please mail From dobbo at thevillas.eclipse.co.uk Wed Jul 14 06:22:35 2004 From: dobbo at thevillas.eclipse.co.uk (rich) Date: Wed, 14 Jul 2004 11:22:35 +0100 (BST) Subject: [BiO BB] mapping swissprot sequence positions to pdb sequence positions Message-ID: <1089800555.40f5096bdac69@webmail.eclipse.net.uk> Hi, could anyone recommend a quick way of mapping the positions in say a swissprot peptide sequence file onto the pdb sequence file? I want to know the actual sequence position values. thanks rich From Piyush.Saggi at appliedbiosystems.com Wed Jul 14 17:12:36 2004 From: Piyush.Saggi at appliedbiosystems.com (Piyush Saggi) Date: Wed, 14 Jul 2004 14:12:36 -0700 Subject: [BiO BB] Invitation to participate in software survey & gift drawing Message-ID: Dear Colleague, The Applied Biosystems Sequencing Software Team.invites you to participate in an online survey to solicit your opinion on currently available software products, their limitations and future direction. Your feedback is of great value in indicating whether we should develop new tools or improve current ones, and what new features to add. The survey should take 10 - 12 minutes. At the end of the survey, please enter your name for a chance to win one of the prizes. Of all respondents who COMPLETE the survey, one lucky winner will receive the grand prize?a choice of an Apple? iPod? MP3 player or Canon? PowerShot? digital camera, and 10 others will each receive a special prize of a USB memory key. In addition, if you are among the first 20 respondents to COMPLETE the survey, we will also send you a surprise early-bird gift. Applied Biosystems invests heavily in R&D, and we want to consider customer feedback into our development process. We realize that you may have answered other surveys from Applied Biosystems and truly appreciate your cooperation in building the future of research tools. Please feel free to contact us for any questions while the survey is open till July 28, 2004. Please click on the link below to access the survey. http://www.appliedbiosystems.com/SeqSoftwareSurvey Thank you very much. Applied Biosystems Sequencing Software Team Please click on the link below to access the survey. http://www.appliedbiosystems.com/SeqSoftwareSurvey For questions/support please contact Piyush Saggi Sequencing Software Development Staff Piyush.Saggi at appliedbiosystems.com (+1)650-638-5475 View Applied Biosystems Privacy Policy. No purchase necessary to enter and win, void where prohibited, must be 18 years of age or older, and the drawing is not open to Applera Corporation employees. No cash equivalents will be given. Offer expires July 28,2004. Applera Corporation is committed to providing the world's leading technology and information for life scientists. Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses. For Research Use Only. Not for use in diagnostic procedures. Applied Biosystems is a registered trademark of Applera Corporation or it subsidiaries in the US and certain other countries. Applied Biosystems 850 Lincoln Centre Drive Foster City, CA 94404 In compliance with Federal regulations, we hereby disclose that this email communication is for commercial purposes. -------------- next part -------------- An HTML attachment was scrubbed... URL: From idoerg at burnham.org Wed Jul 14 19:44:12 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed, 14 Jul 2004 16:44:12 -0700 Subject: [BiO BB] mapping swissprot sequence positions to pdb sequence positions In-Reply-To: <1089800555.40f5096bdac69@webmail.eclipse.net.uk> References: <1089800555.40f5096bdac69@webmail.eclipse.net.uk> Message-ID: <40F5C54C.1060601@burnham.org> A pairwise alignment program, such as blast2seq or EMBOSS's "needle" is probably good for you. I'm not sure I understand your question, is the sequence position coming from the SwissProt file or from the PDB? If the latter, be aware that: 1) PDB sequences contain gaps. 2) Sequence numbers in PDB are non-consecutive even if there are no gaps. 3) Sequence numbering can be alphanumeric and contain insertion codes(e.g. 183, 183A, 183B, 184) 4) Sequecnes can start with negative numbers (e.g. for his-tagged proteins) 5) Mutations abound. Iddo rich wrote: >Hi, > >could anyone recommend a quick way of mapping the >positions in say a swissprot peptide sequence file onto >the pdb sequence file? I want to know the actual >sequence position values. > >thanks >rich >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > From dobbo at thevillas.eclipse.co.uk Thu Jul 15 05:24:10 2004 From: dobbo at thevillas.eclipse.co.uk (rich) Date: Thu, 15 Jul 2004 10:24:10 +0100 (BST) Subject: [BiO BB] mapping swissprot sequence positions to pdb sequence positions In-Reply-To: <40F5C54C.1060601@burnham.org> References: <1089800555.40f5096bdac69@webmail.eclipse.net.uk> <40F5C54C.1060601@burnham.org> Message-ID: <1089883450.40f64d3a43143@webmail.eclipse.net.uk> Hi, yes, thanks. I was thinking about using Align. I am using hssp entries which have a consecutive seqno position. I want to map these values onto the position within the swissprot entry for the protein sequence. I realise that there will be gaps etc in the pdb num but there won't be in the hssp seqno values. effectively i have snps and their positions and i want to map onto the seqno value from the hssp file. The seqno value is simply a consecutive seq position as opposed to the pdb seq position. I think the solution is to run Align on all of my sequences and then parse with Bio::Align, unless there is a quicker way that I haven't thought of cheers Rich thanks Rich Quoting Iddo Friedberg : > > A pairwise alignment program, such as blast2seq > or EMBOSS's "needle" is > probably good for you. > > I'm not sure I understand your question, is the > sequence position coming > from the SwissProt file or from the PDB? If the > latter, be aware that: > > 1) PDB sequences contain gaps. > 2) Sequence numbers in PDB are non-consecutive > even if there are no gaps. > 3) Sequence numbering can be alphanumeric and > contain insertion > codes(e.g. 183, 183A, 183B, 184) > 4) Sequecnes can start with negative numbers > (e.g. for his-tagged proteins) > 5) Mutations abound. > > Iddo > > rich wrote: > > >Hi, > > > >could anyone recommend a quick way of mapping > the > >positions in say a swissprot peptide sequence > file onto > >the pdb sequence file? I want to know the > actual > >sequence position values. > > > >thanks > >rich > >_______________________________________________ > >BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > > > > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > yzman at gwatson.eclipse.co.uk Received: from > mxa02.ex.eclipse.net.uk (mxa02.ex.eclipse.net.uk > [212.104.129.120]) by > mda02.mail.eclipse.net.uk (Postfix) with ESMTP > id 4D5973CC179 for > ; Mon, 12 Jul 2004 > 00:31:12 +0100 (BST) Received: from localhost > (localhost.localdomain [127.0.0.1]) by > mxa02.ex.eclipse.net.uk (Postfix) with ESMTP id > BC0AE34EAB5 for ; > Mon, 12 Jul 2004 00:32:48 +0100 (BST) Received: > from mxa02.ex.eclipse.net.uk ([127.0.0.1]) by > localhost (mxa02.ex.eclipse.net.uk [127.0.0.1]) > (amavisd-new, port 10024) with LMTP id > 15113-01-13 for ; > Mon, 12 Jul 2004 00:32:48 +0100 (BST) Received: > from mx39.smf.ebay.com (mxsmfpool16.ebay.com > [66.135.209.213]) by mxa02.ex.eclipse.net.uk > (Postfix) with ESMTP id 9158134E6E3 for > ; Mon, 12 Jul 2004 > 00:32:47 +0100 (BST) Received: from > sjcbat01.sjc.ebay.com (sjcbat01.sjc.ebay.com > [10.6.37.40]) by mx39.smf.ebay.com > (8.12.3/8.12.3) with ESMTP id > i6BNbVTE015225 for > ; Sun, 11 Jul 2004 > 16:37:35 -0700 Message-Id: > <200407112337.i6BNbVTE015225 at mx39.smf.ebay.com> X-eBay-MailTracker: > 10007.361.3.x To: > yzman at gwatson.eclipse.co.uk From: > dailystatus at ebay.co.uk Mime-Version: > 1.0 Content-Type: multipart/alternative; > boundary="==_MIME-Boundary-1_==" Subject: eBay > Watch List: 11-Jul-04 18:19:45 BST Date: Sun, > 11 Jul 2004 16:36:33 PDT X-Virus-Scanned: by > Eclipse VIRUSshield at eclipse.net.uk > From idoerg at burnham.org Thu Jul 15 20:02:01 2004 From: idoerg at burnham.org (Iddo) Date: Thu, 15 Jul 2004 17:02:01 -0700 Subject: [BiO BB] mapping swissprot sequence positions to pdb sequence positions In-Reply-To: <1089883450.40f64d3a43143@webmail.eclipse.net.uk> References: <1089800555.40f5096bdac69@webmail.eclipse.net.uk> <40F5C54C.1060601@burnham.org> <1089883450.40f64d3a43143@webmail.eclipse.net.uk> Message-ID: <40F71AF9.4090607@burnham.org> Sounds pretty good. Going through the hssp seqno would be my choice too. Be aware that the gaps are marked with a "!", and I _think_ those "!"s are numbered too. (To lazy to look at an HSSP file now). Good luck, Iddo rich wrote: >Hi, yes, thanks. I was thinking about using Align. I am >using hssp entries which have a consecutive seqno >position. I want to map these values onto the position >within the swissprot entry for the protein sequence. I >realise that there will be gaps etc in the pdb num but >there won't be in the hssp seqno values. > >effectively i have snps and their positions and i want >to map onto the seqno value from the hssp file. The >seqno value is simply a consecutive seq position as >opposed to the pdb seq position. > >I think the solution is to run Align on all of my >sequences and then parse with Bio::Align, unless there >is a quicker way that I haven't thought of > >cheers >Rich > >thanks >Rich > >Quoting Iddo Friedberg : > > > >>A pairwise alignment program, such as blast2seq >>or EMBOSS's "needle" is >>probably good for you. >> >>I'm not sure I understand your question, is the >>sequence position coming >>from the SwissProt file or from the PDB? If the >>latter, be aware that: >> >>1) PDB sequences contain gaps. >>2) Sequence numbers in PDB are non-consecutive >>even if there are no gaps. >>3) Sequence numbering can be alphanumeric and >>contain insertion >>codes(e.g. 183, 183A, 183B, 184) >>4) Sequecnes can start with negative numbers >>(e.g. for his-tagged proteins) >>5) Mutations abound. >> >>Iddo >> >>rich wrote: >> >> >> >>>Hi, >>> >>>could anyone recommend a quick way of mapping >>> >>> >>the >> >> >>>positions in say a swissprot peptide sequence >>> >>> >>file onto >> >> >>>the pdb sequence file? I want to know the >>> >>> >>actual >> >> >>>sequence position values. >>> >>>thanks >>>rich >>>_______________________________________________ >>>BiO_Bulletin_Board maillist - >>> >>> >>BiO_Bulletin_Board at bioinformatics.org >> >>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> >>> >>> >>> >>> >>_______________________________________________ >>BiO_Bulletin_Board maillist - >>BiO_Bulletin_Board at bioinformatics.org >> >> >> >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > >>yzman at gwatson.eclipse.co.uk >> >> >Received: from > > >>mxa02.ex.eclipse.net.uk (mxa02.ex.eclipse.net.uk >>[212.104.129.120]) >> >> > by > > >>mda02.mail.eclipse.net.uk (Postfix) with ESMTP >>id 4D5973CC179 >> >> > for > > >>; Mon, 12 Jul 2004 >>00:31:12 +0100 (BST) >> >> >Received: from localhost > > >>(localhost.localdomain [127.0.0.1]) >> >> > by > > >>mxa02.ex.eclipse.net.uk (Postfix) with ESMTP id >>BC0AE34EAB5 >> >> > for ; > > >>Mon, 12 Jul 2004 00:32:48 +0100 (BST) >> >> >Received: > > >>from mxa02.ex.eclipse.net.uk ([127.0.0.1]) >> >> > by > > >>localhost (mxa02.ex.eclipse.net.uk [127.0.0.1]) >>(amavisd-new, port 10024) >> >> > with LMTP id > > >>15113-01-13 for ; >> >> > > > >>Mon, 12 Jul 2004 00:32:48 +0100 (BST) >> >> >Received: > > >>from mx39.smf.ebay.com (mxsmfpool16.ebay.com >>[66.135.209.213]) >> >> > by mxa02.ex.eclipse.net.uk > > >>(Postfix) with ESMTP id 9158134E6E3 >> >> > for > > >>; Mon, 12 Jul 2004 >>00:32:47 +0100 (BST) >> >> >Received: from > > >>sjcbat01.sjc.ebay.com (sjcbat01.sjc.ebay.com >>[10.6.37.40]) >> >> > by mx39.smf.ebay.com > > >>(8.12.3/8.12.3) with ESMTP id >>i6BNbVTE015225 >> >> > for > > >>; Sun, 11 Jul 2004 >>16:37:35 -0700 >> >> >Message-Id: > > >><200407112337.i6BNbVTE015225 at mx39.smf.ebay.com> >> >> >X-eBay-MailTracker: > > >>10007.361.3.x >> >> >To: > > >>yzman at gwatson.eclipse.co.uk >> >> >From: > > >>dailystatus at ebay.co.uk >> >> >Mime-Version: > > >>1.0 >> >> >Content-Type: multipart/alternative; > > >>boundary="==_MIME-Boundary-1_==" >> >> >Subject: eBay > > >>Watch List: 11-Jul-04 18:19:45 BST >> >> >Date: Sun, > > >>11 Jul 2004 16:36:33 PDT >> >> >X-Virus-Scanned: by > > >>Eclipse VIRUSshield at eclipse.net.uk >> >> > > > > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9930 http://ffas.ljcrf.edu/~iddo From dmnunif at charter.net Sat Jul 17 13:48:26 2004 From: dmnunif at charter.net (Unidinium Ltd) Date: 17 Jul 2004 17:48:26 GMT Subject: [BiO BB] "Come visit the Unifinium Website" Message-ID: This email is being sent to you by the web site notification service at EarthLink. You can see our site here: http://www.plantcarebyunifinium.com/bioinformaticsbyunifiniumltd/ This web site was created with Trellix. Build your own web site at http://www.earthlink.net/biz/hosting From Betty.Duncan at mhpcc.hpc.mil Mon Jul 19 18:57:47 2004 From: Betty.Duncan at mhpcc.hpc.mil (Betty Duncan) Date: Mon, 19 Jul 2004 12:57:47 -1000 Subject: [BiO BB] UMUC Message-ID: Does anyone have any experience or comments about the University of Maryland's University College's Masters of Science degree in Biotechnology Studies? Thanks, Betty From rouellette at umuc.edu Tue Jul 20 09:08:12 2004 From: rouellette at umuc.edu (Robert Ouellette) Date: Tue, 20 Jul 2004 09:08:12 -0400 Subject: [BiO BB] UMUC References: Message-ID: <40FD193C.233DF327@umuc.edu> I am sure other will provide you with an evaluation, but as the chair of the Management of Technological system department where the biotechnology program is located , I would like to direct you to our web site www.umuc.edu. We have about 400 master students in bothe The Biotechnology studies programs and the Bioinformatics track. All classes are offered face-to-face and online Regards bob Betty Duncan wrote: > Does anyone have any experience or comments about the University of Maryland's University College's Masters of Science degree in Biotechnology Studies? Thanks, Betty > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- A non-text attachment was scrubbed... Name: rouellette.vcf Type: text/x-vcard Size: 278 bytes Desc: Card for Robert Ouellette URL: From je64p at yahoo.com Thu Jul 22 09:04:43 2004 From: je64p at yahoo.com (=?iso-8859-1?q?Jean-Etienne=20Poirrier?=) Date: Thu, 22 Jul 2004 14:04:43 +0100 (BST) Subject: [BiO BB] Ph.D. in Belgium or MRes in UK? Message-ID: <20040722130443.24943.qmail@web41104.mail.yahoo.com> Hello, I already have a M.D. in biomedical science and I am actually pursuing a Ph.D. in Belgium (2nd of 4 years in fundamental neuroscience, with no practical application). Having an equal interest in computer programming, I wonder if it wouldn't be better for me (future job, well-being, ...) to follow a MRes in bioinformatics during one year, in the UK. In the first case, I would be a Ph.D. in 2 years but no industrial/practical abilities. In the second case, I would be a M.D. in 1 year with (what I think are) more practical abilities. What do you think? I thank you in advance. Yours sincerely, JEtienne ___________________________________________________________ALL-NEW Yahoo! Messenger - sooooo many all-new ways to express yourself http://uk.messenger.yahoo.com From yzz100 at psu.edu Thu Jul 22 20:37:38 2004 From: yzz100 at psu.edu (Ya Zhang) Date: Thu, 22 Jul 2004 17:37:38 -0700 Subject: [BiO BB] Non-redudant swissprot protein sequences In-Reply-To: <20040720160111.38447D1F3A@www.bioinformatics.org> References: <20040720160111.38447D1F3A@www.bioinformatics.org> Message-ID: <41005DD2.3080508@psu.edu> Does anyone know where can I download swissprot prtein sequences with similarity lower than 95% to each other? I know the ASTRAL has such type of dataset for PDB sequences. Is there anyone know how to make the dataset? Thanks! Ya From dmnunif at charter.net Thu Jul 22 21:00:07 2004 From: dmnunif at charter.net (D. Norris) Date: Thu, 22 Jul 2004 20:00:07 -0500 Subject: [BiO BB] Ph.D. in Belgium or MRes in UK? References: <20040722130443.24943.qmail@web41104.mail.yahoo.com> Message-ID: <000b01c47050$65e88b90$c37db118@VALUED4DA88152> JEtienne: I am responding to your inquiry regarding other peoples' thoughts about what educational direction(s) you should pursue. I do this only because I was a research professor for 40 years, and learned that people (my students and post-docs) seemed to both have a more positive personal life, and contribute more in science(and/or medicine), if they unfailing followed their strongest interests (i.e., strongest motivations). Do "your thing (s)", and let the "chips" fall as they may !! dmn ----- Original Message ----- From: "Jean-Etienne Poirrier" To: Sent: Thursday, July 22, 2004 8:04 AM Subject: [BiO BB] Ph.D. in Belgium or MRes in UK? > Hello, > > I already have a M.D. in biomedical science and I am > actually pursuing a Ph.D. in Belgium (2nd of 4 years > in fundamental neuroscience, with no practical > application). Having an equal interest in computer > programming, I wonder if it wouldn't be better for me > (future job, well-being, ...) to follow a MRes in > bioinformatics during one year, in the UK. > > In the first case, I would be a Ph.D. in 2 years but > no industrial/practical abilities. In the second case, > I would be a M.D. in 1 year with (what I think are) > more practical abilities. > > What do you think? > I thank you in advance. > Yours sincerely, > JEtienne > > > > > > ___________________________________________________________ALL-NEW Yahoo! Messenger - sooooo many all-new ways to express yourself http://uk.messenger.yahoo.com > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From idoerg at burnham.org Thu Jul 22 21:59:06 2004 From: idoerg at burnham.org (Iddo) Date: Thu, 22 Jul 2004 18:59:06 -0700 Subject: [BiO BB] Non-redudant swissprot protein sequences In-Reply-To: <41005DD2.3080508@psu.edu> References: <20040720160111.38447D1F3A@www.bioinformatics.org> <41005DD2.3080508@psu.edu> Message-ID: <410070EA.6060203@burnham.org> How about downloading the entire SWISSPROT and then clustering it yourself using CD-HIT? http://bioinformatics.org/cd-hit/ Iddo Ya Zhang wrote: > Does anyone know where can I download swissprot prtein sequences with > similarity lower than 95% to each other? I know the ASTRAL has such > type of dataset for PDB sequences. Is there anyone know how to make the > dataset? > > Thanks! > > Ya > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9930 http://ffas.ljcrf.edu/~iddo From pooja at igc.gulbenkian.pt Fri Jul 23 04:14:43 2004 From: pooja at igc.gulbenkian.pt (Pooja Jain) Date: Fri, 23 Jul 2004 09:14:43 +0100 (WEST) Subject: [BiO BB] GRN Construction In-Reply-To: References: Message-ID: <2001.203.129.192.23.1090570483.squirrel@webmail.igc.gulbenkian.pt> Hi, Does anybody knows about software similar to PathwayAssist (by Ariadne Genomics) to re-engineere biological pathways (in particular Genetic Regulatory Networks (GRNs)) or interaction networks from expression data? www.ariadnegenomics.com/products/pathway.html Thank you in advance, -Pooja From dmb at mrc-dunn.cam.ac.uk Fri Jul 23 08:55:57 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 23 Jul 2004 13:55:57 +0100 (BST) Subject: [BiO BB] Non-redudant swissprot protein sequences In-Reply-To: <410070EA.6060203@burnham.org> Message-ID: They do this already at uniprot, which is nice. It is a service called 'uniref'. ftp://ftp.ebi.ac.uk/pub/databases/uniprot/uniref/ You can get 100, 90 and 50% nr, where the 90 set is derived from the 100 set (via a two step process), and 50 is derived from 90 via a three step process. I still haven't quite got my head round the way they handle varsplic in uniref with relation to uniprot. It is probably documented though. Cheers, On Thu, 22 Jul 2004, Iddo wrote: > >How about downloading the entire SWISSPROT and then clustering it >yourself using CD-HIT? > >http://bioinformatics.org/cd-hit/ > >Iddo > > >Ya Zhang wrote: > >> Does anyone know where can I download swissprot prtein sequences with >> similarity lower than 95% to each other? I know the ASTRAL has such >> type of dataset for PDB sequences. Is there anyone know how to make the >> dataset? >> >> Thanks! >> >> Ya >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> > > > From aroman6 at alumno.uned.es Fri Jul 23 11:15:53 2004 From: aroman6 at alumno.uned.es (ANGEL CARLOS ROMAN GARCI) Date: Fri, 23 Jul 2004 17:15:53 +0200 (CEST) Subject: [BiO BB] installing blast Message-ID: <8395.213.0.156.106.1090595753.squirrel@213.0.156.106> I've got a problem with the Standalone BLAST; after I unzip and untar it, I put the .ncbirc file with [NCBI] Data="mypath/data" and I unzip a db (Fasta preformatted); right now, it should work, but no command is recognized in the console. neither blastall, nor the others (but these commands exists in the directory). could you help me? Thanks From landman at scalableinformatics.com Fri Jul 23 11:28:35 2004 From: landman at scalableinformatics.com (Joe Landman) Date: Fri, 23 Jul 2004 11:28:35 -0400 Subject: [BiO BB] installing blast In-Reply-To: <8395.213.0.156.106.1090595753.squirrel@213.0.156.106> References: <8395.213.0.156.106.1090595753.squirrel@213.0.156.106> Message-ID: <41012EA3.1000109@scalableinformatics.com> Hi Angel: You need to make sure that blastall is in your path. Try this: which blastall If it is working properly, you should see something like this: hammer:~ # which blastall /usr/bin/blastall You may need to edit your .cshrc or .bashrc to reflect the path to BLAST. If you prefer to use an RPM for installation, feel free to grab them from http://downloads.scalableinformatics.com/downloads/ncbi/ . Joe ANGEL CARLOS ROMAN GARCI wrote: > I've got a problem with the Standalone BLAST; > > after I unzip and untar it, I put the .ncbirc file with > [NCBI] > Data="mypath/data" > > and I unzip a db (Fasta preformatted); > > right now, it should work, but no command is recognized in the console. > neither blastall, nor the others (but these commands exists in the > directory). > > could you help me? > Thanks > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Joe Landman Scalable Informatics LLC email: landman at scalableinformatics.com web : http://scalableinformatics.com phone: +1 734 612 4615 From aroman6 at alumno.uned.es Fri Jul 23 12:05:50 2004 From: aroman6 at alumno.uned.es (ANGEL CARLOS ROMAN GARCI) Date: Fri, 23 Jul 2004 18:05:50 +0200 (CEST) Subject: [BiO BB] installing blast In-Reply-To: <41012EA3.1000109@scalableinformatics.com> References: <8395.213.0.156.106.1090595753.squirrel@213.0.156.106> <41012EA3.1000109@scalableinformatics.com> Message-ID: <11319.213.0.155.194.1090598750.squirrel@213.0.155.194> k, when i write which blastall I obtain: /usr/bin/which : no blastall in (/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin....)(and so) how can I fix the error? From landman at scalableinformatics.com Fri Jul 23 12:17:24 2004 From: landman at scalableinformatics.com (Joe Landman) Date: Fri, 23 Jul 2004 12:17:24 -0400 Subject: [BiO BB] installing blast In-Reply-To: <11319.213.0.155.194.1090598750.squirrel@213.0.155.194> References: <8395.213.0.156.106.1090595753.squirrel@213.0.156.106> <41012EA3.1000109@scalableinformatics.com> <11319.213.0.155.194.1090598750.squirrel@213.0.155.194> Message-ID: <41013A14.6060504@scalableinformatics.com> ANGEL CARLOS ROMAN GARCI wrote: > k, when i write > which blastall > I obtain: > /usr/bin/which : no blastall in > (/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin....)(and so) > > how can I fix the error? you need to look at your path: [landman at protein:~] 70 >env | grep -i "^path" PATH=/opt/kde3/bin:/opt/gnome/bin:/usr/games:/home/landman/bin:/usr/bin/X11:/usr/local/bin:/usr/bin:/usr/X11R6/bin:/bin:/usr/lib/java/bin:/usr/etc:/sbin:/usr/sbin:/home/landman/office/program:/home/landman/Komodo-2.3:/usr/lib/java/bin:/usr/local/bin:/usr/etc:/sbin:/usr/sbin:/home/landman/office/program:/home/landman/Komodo-2.3 and place the blastall binary into one of those directories, or extend your path (shell dependent, see below) to include the directory where you placed blastall To extend your path, first note the directory where you placed blastall. Lets call this (for the sake of this discussion) /path/to/blast/binaries/ If you are using csh/tcsh, you can do the following set path = ( $path /path/to/blast/binaries/ ) and you will have to manually type "rehash" after doing this. If you are using bash/sh, you can do the following export PATH=$PATH:/path/to/blast/binaries/ You may place these commands (except for the rehash) into your .cshrc or .bashrc. After setting the path, retry the which. It should work, unless you also need to chmod 755 /path/to/blast/binaries/blastall Joe -- Joe Landman Scalable Informatics LLC email: landman at scalableinformatics.com web : http://scalableinformatics.com phone: +1 734 612 4615 From idoerg at burnham.org Fri Jul 23 13:07:34 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Fri, 23 Jul 2004 10:07:34 -0700 Subject: [BiO BB] installing blast In-Reply-To: <11319.213.0.155.194.1090598750.squirrel@213.0.155.194> References: <8395.213.0.156.106.1090595753.squirrel@213.0.156.106> <41012EA3.1000109@scalableinformatics.com> <11319.213.0.155.194.1090598750.squirrel@213.0.155.194> Message-ID: <410145D6.3000301@burnham.org> The information in ~/.ncbirc points to the data files used by the blast program suite, not to the programs themselves. For that there is the PATH shell variable. You should add the location of blastall to your path, in your .cshrc or .bashrc depending on the shell you are using. e.g. ad to your .cshrc file the following line: setenv PATH = ${PATH}:/path/to/blastall And then open a new shell to make in effective, or run source ~/.cshrc in an old shell. It's probly a good idea to get a basic Linux/Unix tutorial book. Seems like your problems stem from being unfamiliar with the operating system. HTH, Iddo ANGEL CARLOS ROMAN GARCI wrote: >k, when i write >which blastall >I obtain: >/usr/bin/which : no blastall in >(/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin....)(and so) > >how can I fix the error? > > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 North Torrey Pines Road La Jolla, CA 92037 USA T: (858) 646 3100 x3516 F: (858) 713 9930 http://ffas.ljcrf.edu/~iddo From dobbo at thevillas.eclipse.co.uk Wed Jul 21 10:18:50 2004 From: dobbo at thevillas.eclipse.co.uk (rich) Date: Wed, 21 Jul 2004 15:18:50 +0100 (BST) Subject: [BiO BB] mapping swissprot sequence positions to pdb sequence positions In-Reply-To: <40F71AF9.4090607@burnham.org> References: <1089800555.40f5096bdac69@webmail.eclipse.net.uk> <40F5C54C.1060601@burnham.org> <1089883450.40f64d3a43143@webmail.eclipse.net.uk> <40F71AF9.4090607@burnham.org> Message-ID: <1090419530.40fe7b4a04974@webmail.eclipse.net.uk> ah, yes, not sure how to get around this..... Quoting Iddo : > > Sounds pretty good. Going through the hssp seqno > would be my choice too. > Be aware that the gaps are marked with a "!", > and I _think_ those "!"s > are numbered too. (To lazy to look at an HSSP > file now). > > Good luck, > > Iddo > > > rich wrote: > > >Hi, yes, thanks. I was thinking about using > Align. I am > >using hssp entries which have a consecutive > seqno > >position. I want to map these values onto the > position > >within the swissprot entry for the protein > sequence. I > >realise that there will be gaps etc in the pdb > num but > >there won't be in the hssp seqno values. > > > >effectively i have snps and their positions and > i want > >to map onto the seqno value from the hssp file. > The > >seqno value is simply a consecutive seq > position as > >opposed to the pdb seq position. > > > >I think the solution is to run Align on all of > my > >sequences and then parse with Bio::Align, > unless there > >is a quicker way that I haven't thought of > > > >cheers > >Rich > > > >thanks > >Rich > > > >Quoting Iddo Friedberg : > > > > > > > >>A pairwise alignment program, such as > blast2seq > >>or EMBOSS's "needle" is > >>probably good for you. > >> > >>I'm not sure I understand your question, is > the > >>sequence position coming > >>from the SwissProt file or from the PDB? If > the > >>latter, be aware that: > >> > >>1) PDB sequences contain gaps. > >>2) Sequence numbers in PDB are > non-consecutive > >>even if there are no gaps. > >>3) Sequence numbering can be alphanumeric > and > >>contain insertion > >>codes(e.g. 183, 183A, 183B, 184) > >>4) Sequecnes can start with negative numbers > >>(e.g. for his-tagged proteins) > >>5) Mutations abound. > >> > >>Iddo > >> > >>rich wrote: > >> > >> > >> > >>>Hi, > >>> > >>>could anyone recommend a quick way of > mapping > >>> > >>> > >>the > >> > >> > >>>positions in say a swissprot peptide > sequence > >>> > >>> > >>file onto > >> > >> > >>>the pdb sequence file? I want to know the > >>> > >>> > >>actual > >> > >> > >>>sequence position values. > >>> > >>>thanks > >>>rich > >>>_______________________________________________ > >>>BiO_Bulletin_Board maillist - > >>> > >>> > >>BiO_Bulletin_Board at bioinformatics.org > >> > >>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > >> > >> > >>> > >>> > >>> > >>> > >>_______________________________________________ > >>BiO_Bulletin_Board maillist - > >>BiO_Bulletin_Board at bioinformatics.org > >> > >> > >> > >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > >>yzman at gwatson.eclipse.co.uk > >> > >> > >Received: from > > > > > >>mxa02.ex.eclipse.net.uk > (mxa02.ex.eclipse.net.uk > >>[212.104.129.120]) > >> > >> > > by > > > > > >>mda02.mail.eclipse.net.uk (Postfix) with > ESMTP > >>id 4D5973CC179 > >> > >> > > for > > > > > >>; Mon, 12 Jul > 2004 > >>00:31:12 +0100 (BST) > >> > >> > >Received: from localhost > > > > > >>(localhost.localdomain [127.0.0.1]) > >> > >> > > by > > > > > >>mxa02.ex.eclipse.net.uk (Postfix) with ESMTP > id > >>BC0AE34EAB5 > >> > >> > > for ; > > > > > >>Mon, 12 Jul 2004 00:32:48 +0100 (BST) > >> > >> > >Received: > > > > > >>from mxa02.ex.eclipse.net.uk ([127.0.0.1]) > >> > >> > > by > > > > > >>localhost (mxa02.ex.eclipse.net.uk > [127.0.0.1]) > >>(amavisd-new, port 10024) > >> > >> > > with LMTP id > > > > > >>15113-01-13 for > ; > >> > >> > > > > > > > >>Mon, 12 Jul 2004 00:32:48 +0100 (BST) > >> > >> > >Received: > > > > > >>from mx39.smf.ebay.com (mxsmfpool16.ebay.com > >>[66.135.209.213]) > >> > >> > > by mxa02.ex.eclipse.net.uk > > > > > >>(Postfix) with ESMTP id 9158134E6E3 > >> > >> > > for > > > > > >>; Mon, 12 Jul > 2004 > >>00:32:47 +0100 (BST) > >> > >> > >Received: from > > > > > >>sjcbat01.sjc.ebay.com (sjcbat01.sjc.ebay.com > >>[10.6.37.40]) > >> > >> > > by mx39.smf.ebay.com > > > > > >>(8.12.3/8.12.3) with ESMTP id > >>i6BNbVTE015225 > >> > >> > > for > > > > > >>; Sun, 11 Jul > 2004 > >>16:37:35 -0700 > >> > >> > >Message-Id: > > > > > >><200407112337.i6BNbVTE015225 at mx39.smf.ebay.com> > >> > >> > >X-eBay-MailTracker: > > > > > >>10007.361.3.x > >> > >> > >To: > > > > > >>yzman at gwatson.eclipse.co.uk > >> > >> > >From: > > > > > >>dailystatus at ebay.co.uk > >> > >> > >Mime-Version: > > > > > >>1.0 > >> > >> > >Content-Type: multipart/alternative; > > > > > >>boundary="==_MIME-Boundary-1_==" > >> > >> > >Subject: eBay > > > > > >>Watch List: 11-Jul-04 18:19:45 BST > >> > >> > >Date: Sun, > > > > > >>11 Jul 2004 16:36:33 PDT > >> > >> > >X-Virus-Scanned: by > > > > > >>Eclipse VIRUSshield at eclipse.net.uk > >> > >> > > > > > > > > > >_______________________________________________ > >BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > > > > > > -- > Iddo Friedberg, Ph.D. > The Burnham Institute > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037 USA > Tel: +1 (858) 646 3100 x3516 > Fax: +1 (858) 713 9930 > http://ffas.ljcrf.edu/~iddo > > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From katia at cin.ufpe.br Wed Jul 21 19:05:56 2004 From: katia at cin.ufpe.br (Katia Silva Guimaraes) Date: Wed, 21 Jul 2004 20:05:56 -0300 (EST) Subject: [BiO BB] CompBioNets 2004 Message-ID: CompBioNets 2004 Algorithms and Computational Methods for Biochemical and Evolutionary Networks Recife, BRAZIL, December 15-18, 2004 CALL FOR PAPERS We wish to invite you to submit a paper to the Conference "Algorithms and Computational Methods for Biochemical and Evolutionary Networks" (CompBioNets'04) that is being organized in Recife, Brazil, December 15-18, 2004. The conference topics will be computational biology in general, and more specifically, but not exclusively, genetic regulation, motifs, metabolism, protein-protein interaction, biochemical networks, protein function and structure, genome dynamics, genome rearrangements, comparative genomics. Submitted papers will be selected by an international Program Committee. Accepted papers will be presented in a 25 minutes talk and will appear in the form of a book published by "KCL publications", London, which will be available at the Conference. The authors of the best papers will be invited to submit their work for publication in a special issue of Journal of Discrete Algorithms, Elsevier. A call for posters will be made later. The Conference has its origin in a long-standing collaboration between a Brazilian from the Federal University of Pernambuco, Recife, and a Brazilian at large. The Conference will follow a rigorous paper selection process and include high-ranking invited talks. At the same time, it is hoped that it will have a nice familiar atmosphere reflecting both the country's warm-hearted and joyful spirit and the friendship behind the collaboration that gave birth to the Conference. Recife, the city where the Conference will be held, is a most lovely city located in the Northeast of Brazil. The temperature there stays around 86F (30C) all year long, but the air is kept cool by the wind coming from the sea. In Recife itself and near the town, are some of the most beautiful beaches in Brazil, including Porto de Galinhas Beach, a natural pool type of beach, with beautiful colorful little fishes. Just 8 miles from Recife is the historical town of Olinda (in portuguese, the town's name means "Oh beautiful!"), one of the oldest cities in Brazil. The harmonious balance between the buildings, gardens, 20 Baroque churches, convents and numerous small "passos" (chapels) all contribute to Olinda's particular charm. Additional information can be found in the conference webpage: http://compbionets.cin.ufpe.br. _______________________________________________________________ From Sheryl at uq.edu.au Thu Jul 22 02:18:23 2004 From: Sheryl at uq.edu.au (Sheryl Maher) Date: Thu, 22 Jul 2004 16:18:23 +1000 Subject: [BiO BB] Clustalx error Message-ID: <003e01c46fb3$c6c98060$c1dfa8c0@SHEDDY> Hi, I am attempting to get clustal X working under window, I am not sure if it is designed to work in this environment or not. I am getting an error when I attempt to do a multiple alignment, that is is unable to access the .aln file. I am not sure if anyone else has experianced this and found a work around. Thanks Sheryl Maher -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael_jennings at mail.ru Thu Jul 22 19:57:01 2004 From: michael_jennings at mail.ru (Michael Jennings) Date: Fri, 23 Jul 2004 03:57:01 +0400 Subject: [BiO BB] Ph.D. in Belgium or MRes in UK=?koi8-r?Q?=3F?= In-Reply-To: <20040722130443.24943.qmail@web41104.mail.yahoo.com> Message-ID: > Hello, Hello Back~! > I already have a M.D. in biomedical science and I am > actually pursuing a Ph.D. in Belgium (2nd of 4 years > in fundamental neuroscience, with no practical > application). Having an equal interest in computer > programming, I wonder if it wouldn't be better for me > (future job, well-being, ...) to follow a MRes in > bioinformatics during one year, in the UK. That's a tough one ... but I wouldn't quit your PhD just yet ... you can manouever inside the topic? > In the first case, I would be a Ph.D. in 2 years but > no industrial/practical abilities. In the second case, > I would be a M.D. in 1 year with (what I think are) > more practical abilities. I've seen plenty of PhDs that have no practical application - that is not the point. The PhD is a piece of paper that states that you have joined the 'club'. I quite mine in nuclear physics to study in biotech (duh~!) Nuc was boring - and not particualr safe (lots of DS breaks) ... and most graduates went on to be computer programmers ... or public servants. It wasn't even the industry that someone with half a brain would want to work in .... > What do you think? I would rework your topic - submit it - and then go and retrain in whatever you want. A PhD represents what you know about a particular topic at a certain point in time. They are potential fickle - and troublesome. Get it - and get out. Then the world is your Oyster~! Regards, Mike From cmoita at igc.gulbenkian.pt Mon Jul 26 16:36:27 2004 From: cmoita at igc.gulbenkian.pt (Catarina S. F. Moita) Date: Mon, 26 Jul 2004 21:36:27 +0100 (WEST) Subject: [BiO BB] Re: BiO_BB, Clustalx error In-Reply-To: <20040726160105.31F0DD1F00@www.bioinformatics.org> References: <20040726160105.31F0DD1F00@www.bioinformatics.org> Message-ID: <3116.213.13.51.156.1090874187.squirrel@webmail.igc.gulbenkian.pt> > Message: 3 > From: "Sheryl Maher" > To: > Date: Thu, 22 Jul 2004 16:18:23 +1000 > Subject: [BiO BB] Clustalx error > Reply-To: bio_bulletin_board at bioinformatics.org > Hi, Sheryl! > > Hi,=20 > > I am attempting to get clustal X working under window, I am not sure if = > it is designed to work in this environment or not.=20 I've used Clustal X under Windows operating system, and never had any kind of problem. > I am getting an error when I attempt to do a multiple alignment, that is = > is unable to access the .aln file. I am not sure if anyone else has = > experianced this and found a work around.=20 I'm not sure what's the problem you've been facing, but you're supposed to "load" a simple .txt file with your sequences in Fasta format (or other accepted format) into Clustal and perform the multiple alignment. Nevertheless, check http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html Hope that helps, Catarina Moita. > Thanks > > Sheryl Maher From ehrlich at zib.de Tue Jul 27 08:45:09 2004 From: ehrlich at zib.de (Christian Ehrlich) Date: Tue, 27 Jul 2004 14:45:09 +0200 Subject: [BiO BB] Where to get a test-set from DSSP? Message-ID: <129363605.20040727144509@zib.de> Hi I am looking for a test-set which constains the AASequence and the HSSP Secondary Structure. The file should be row based and not columb based like the usual DSSP output. Does anyone have this kind of set or knows were I could get it. Thx -- Mit freudlichen Gr?sse Christian Ehrlich mailto:ehrlich at zib.de ZIB / CSR Tel: +49 30 84185-405 From ehrlich at zib.de Tue Jul 27 10:58:47 2004 From: ehrlich at zib.de (Christian Ehrlich) Date: Tue, 27 Jul 2004 16:58:47 +0200 Subject: [BiO BB] getting the SWISSPROT ID from the PDB ID Message-ID: <131162643.20040727165847@zib.de> anyone any ideas how i could do this whith very less circumstances? -- Mit freudlichen Gr?ssen Christian Ehrlich mailto:ehrlich at zib.de ZIB / CSR Tel: +49 30 84185-405 From lhewei at TripathImaging.com Wed Jul 28 13:35:28 2004 From: lhewei at TripathImaging.com (Li, Hewei) Date: Wed, 28 Jul 2004 13:35:28 -0400 Subject: [BiO BB] RE: getting the SWISSPROT ID from the PDB ID Message-ID: <82A249294A811342BD83C8395FEEFFBF2FA3AC@tpe-exch.tripathimaging.com> Christian, There is a direct link from PDB ID to SWISSPROT ID: >From the PDB page, click "Sequence Details" on the left-hand side, which brings you to a "Tabular Overview", in the end of the table, a DBREF column contains the SWISSPROT links for the given protein(s). Hope it helps, Thanks, Hewei Li, MD, PhD North Carolina, USA -----Original Message----- From: bio_bulletin_board-request at bioinformatics.org [mailto:bio_bulletin_board-request at bioinformatics.org] Sent: Wednesday, July 28, 2004 12:01 PM Date: Tue, 27 Jul 2004 16:58:47 +0200 From: Christian Ehrlich Organization: ZIB / CSR To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] getting the SWISSPROT ID from the PDB ID Reply-To: bio_bulletin_board at bioinformatics.org anyone any ideas how i could do this whith very less circumstances? -- Mit freudlichen Gr?ssen Christian Ehrlich mailto:ehrlich at zib.de ZIB / CSR Tel: +49 30 84185-405