From ext29 at eecs.cwru.edu Wed Jun 1 21:40:27 2005 From: ext29 at eecs.cwru.edu (Eray Tuzun) Date: Wed, 1 Jun 2005 21:40:27 -0400 (EDT) Subject: [BiO BB] Parsing NCBI-BLAST -m 3 or -m 4 option In-Reply-To: References: Message-ID: I'd like to parse NCBI-Blast -m 3 option or -m 4 option. Is there any open source programs for this?(C,Java or Perl) Thanks, Eray ERAY TUZUN, MS Senior Computer Specialist Department of Genome Sciences University of Washington From idoerg at burnham.org Wed Jun 1 23:46:16 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed, 1 Jun 2005 20:46:16 -0700 Subject: [BiO BB] Parsing NCBI-BLAST -m 3 or -m 4 option In-Reply-To: Message-ID: Eray, Check out bioperl.org / biojava.org for BLAST parsers. Biopython has good BLAST parsers, but Python was not on your language list. HTH, 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) 646 3171 http://ffas.ljcrf.edu/~iddo ------------------------------------- Automated Protein Function Prediction Meeting, June 24, 2005 http://ffas.burnham.org/AFP On Wed, 1 Jun 2005, Eray Tuzun wrote: > > > I'd like to parse NCBI-Blast -m 3 option or -m 4 option. Is there any open > source programs for this?(C,Java or Perl) > > Thanks, > Eray > > > ERAY TUZUN, MS > Senior Computer Specialist > Department of Genome Sciences > University of Washington > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From 10072214 at hope.ac.uk Thu Jun 2 13:17:58 2005 From: 10072214 at hope.ac.uk (SUJITA PURUSHOTHAMAN) Date: Thu, 02 Jun 2005 18:17:58 +0100 Subject: [BiO BB] Request for impartial opinion Message-ID: Hello, I recently submitted a piece of academic work, and am not happy with the grading I was given. I believe the examiner was not familiar with the topic, bioinformatics. I'd like to know how good/bad it is from another source for the sake of personal satisfaction, hence if someone familiar with the topic has the time to read through the thesis and give me their opinion, I'd be grateful. Please reply to me (not the board). Thanks! -Sujita From veredcc at bgumail.bgu.ac.il Fri Jun 3 01:53:40 2005 From: veredcc at bgumail.bgu.ac.il (Vered Caspi) Date: Fri, 3 Jun 2005 8:53:40 +0300 Subject: [BiO BB] A database system for in-house sequence collections Message-ID: <20050603054637.5145333E62@smtp2.bgu.ac.il> I am looking for a freely available software for storage (preferably in MySQL), management and batch analysis of collections of sequences and their annotations. The sequences are usually generated in-house by various research groups. We can currently allocate a single Linux server for this purpose. Any advice will be highly welcome. Vered === Vered Caspi, Ph.D. Bioinformatics Support Unit, Head National Institute for Biotechnology in the Negev, Building 39, room 214 Ben-Gurion University of the Negev Beer-Sheva 84105, Israel Email: veredcc at bgumail.bgu.ac.il Tel: 08-6479034 054-7915969 From vnadeem at gmail.com Fri Jun 3 05:49:32 2005 From: vnadeem at gmail.com (V.Nadeem Ahmad) Date: Fri, 3 Jun 2005 15:19:32 +0530 Subject: [BiO BB] Request for impartial opinion In-Reply-To: References: Message-ID: good...feelings.... could you send me the thesis to have a look regards, Nadeem On 6/2/05, SUJITA PURUSHOTHAMAN <10072214 at hope.ac.uk> wrote: > > Hello, > I recently submitted a piece of academic work, and am not happy > with the grading I was given. I believe the examiner was not familiar > with the topic, bioinformatics. I'd like to know how good/bad it is from > another source for the sake of personal satisfaction, hence if someone > familiar with the topic has the time to read through the thesis and give > me their opinion, I'd be grateful. Please reply to me (not the board). > Thanks! > -Sujita > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- ======================= V.Nadeem Ahmad B.Tech.,PGD Computational Chemistry,R&D AstraZeneca India Ltd Bangalore,INDIA Mobile: +919886580590 ======================= "we go round the ring and suppose.................... .............but secret sits in the middle and knows" -------------- next part -------------- An HTML attachment was scrubbed... URL: From operon at cbiot.ufrgs.br Fri Jun 3 08:46:12 2005 From: operon at cbiot.ufrgs.br (Marcos Oliveira de Carvalho) Date: Fri, 03 Jun 2005 09:46:12 -0300 Subject: [BiO BB] A database system for in-house sequence collections In-Reply-To: <20050603054637.5145333E62@smtp2.bgu.ac.il> References: <20050603054637.5145333E62@smtp2.bgu.ac.il> Message-ID: Hi Vered, I have tested and used Sabia (http://www.sabia.lncc.br/), GenDb (http://www.cebitec.uni-bielefeld.de/groups/brf/software/gendb_info/) and Manatee (http://manatee.sourceforge.net/) for microbial genome management and annotation (all are good tools, I recommend that you try each and see what fits better to your needs). For EST sequences I found StackPack (http://www.sanbi.ac.za/CODES/STACKPACK_REQUEST/) very useful. If you are looking systems for more complex genomes, you should try GMOD (http://www.gmod.org/) and ENSEMBL (http://www.ensembl.org/) Cheers Marcos On Fri, 03 Jun 2005 05:03:00 -0300, Vered Caspi wrote: > I am looking for a freely available software for storage (preferably in > MySQL), management and batch analysis of collections of sequences and > their annotations. The sequences are usually generated in-house by > various research groups. > We can currently allocate a single Linux server for this purpose. > Any advice will be highly welcome. > Vered > > === > Vered Caspi, Ph.D. > Bioinformatics Support Unit, Head > National Institute for Biotechnology in the Negev, > Building 39, room 214 > Ben-Gurion University of the Negev > Beer-Sheva 84105, Israel > Email: veredcc at bgumail.bgu.ac.il > Tel: 08-6479034 054-7915969 > > > > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From vsmathur at UTMB.EDU Fri Jun 3 10:30:08 2005 From: vsmathur at UTMB.EDU (Mathura, Venkatarajan S.) Date: Fri, 3 Jun 2005 09:30:08 -0500 Subject: [BiO BB] Articles invited for a Bioinformatics book Message-ID: Articles are invited for a book titled "Introduction to Bioinformatics: A workbook approach" to be published by Springer. The book is expected to be published by the end of this year. If you have an interesting Bioinformatics application, please include a short manuscript (1-2 pages) using the format enclosed. For details and your intent to write please contact: Venkat Mathura (venkat at rfdn.org) Details and Format: Book title Introduction to Bioinformatics: A workbook approach Targeted audience Undergraduate and graduate students Publisher Springer Date to be published End of 2005 Corresponding Editor Venkat Mathura Roskamp Institute Sarasota, FL 34243 USA Email: venkat at rfdn.org Phone: 9417522949 How to contribute 1-2 pages about an Application/Tool/Software package in Bioinformatics can be submitted in the following format: Author and Affiliation: eg. John Doe Center for Biocomputing University of Texas Austin Austin, Texas Application/Tool/Package name: ClustalNew (v 1.0) Short Introduction & Algorithm: Include algorithms used in the tool or proved citation of paper published. Detail features available in the tool References should be (author, year) style. If there are more than two authors use et al. Availability (web site): http://newsite.bioinfo.org/ClustalNew.html Application in Bioinformatics To perform multiple alignment of protein or DNA sequences??. Usage (give a biological application or an example) We will describe here how to create multiple alignment of SH3 domain protein?.. Exercise (include one or more question to which the student should address) Perform a multiple aligment of the following sequence (genbank_id1, genbank_id2) and identify conserved segments???. Figure legends and tables Figure 1. Screen capture of multiple alignment???. References Doe J. ?ClustalNew: A fast multiple sequence alignment tool? J computational Biology 2005 33:192-193 Note 1. Please check with the editors regarding suitability of your application. 2. The editors reserve rights to add, delete, reformat or exclude contents. 3. Articles that do not meet scientific standards will be rejected. 4. You may write about applications developed by others (to reduce redundancy please check with the editor) 5. Reference style should be consistent. 6. Figures and tables should be numbered appropriately. 7. Please submit your manuscript as word document (double spaced) by email to venkat at rfdn.org. 8. The authors will be notified about the acceptance and inclusion in the book as soon as possible. 9. For questions please contact: venkat at rfdn.org -----Original Message----- From: bio_bulletin_board-bounces+vsmathur=utmb.edu at bioinformatics.org on behalf of bio_bulletin_board-request at bioinformatics.org Sent: Thu 6/2/2005 11:07 AM To: bio_bulletin_board at bioinformatics.org Cc: Subject: BiO_Bulletin_Board Digest, Vol 8, Issue 1 Send BiO_Bulletin_Board mailing list submissions to bio_bulletin_board at bioinformatics.org To subscribe or unsubscribe via the World Wide Web, visit https://bioinformatics.org/mailman/listinfo/bio_bulletin_board or, via email, send a message with subject or body 'help' to bio_bulletin_board-request at bioinformatics.org You can reach the person managing the list at bio_bulletin_board-owner at bioinformatics.org When replying, please edit your Subject line so it is more specific than "Re: Contents of BiO_Bulletin_Board digest..." Today's Topics: 1. Parsing NCBI-BLAST -m 3 or -m 4 option (Eray Tuzun) 2. Re: Parsing NCBI-BLAST -m 3 or -m 4 option (Iddo Friedberg) ---------------------------------------------------------------------- Message: 1 Date: Wed, 1 Jun 2005 21:40:27 -0400 (EDT) From: Eray Tuzun Subject: [BiO BB] Parsing NCBI-BLAST -m 3 or -m 4 option To: "The general forum at Bioinformatics.Org" Message-ID: Content-Type: text/plain; charset=us-ascii I'd like to parse NCBI-Blast -m 3 option or -m 4 option. Is there any open source programs for this?(C,Java or Perl) Thanks, Eray ERAY TUZUN, MS Senior Computer Specialist Department of Genome Sciences University of Washington ------------------------------ Message: 2 Date: Wed, 1 Jun 2005 20:46:16 -0700 From: Iddo Friedberg Subject: Re: [BiO BB] Parsing NCBI-BLAST -m 3 or -m 4 option To: "The general forum at Bioinformatics.Org" Cc: ext29 at eecs.cwru.edu Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII Eray, Check out bioperl.org / biojava.org for BLAST parsers. Biopython has good BLAST parsers, but Python was not on your language list. HTH, Iddo -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA Tel: ? (858) 646 3100 x3516 Fax: ? (858) 646 3171 http://ffas.ljcrf.edu/~iddo ------------------------------------- Automated Protein Function Prediction Meeting, June 24, 2005 http://ffas.burnham.org/AFP On Wed, 1 Jun 2005, Eray Tuzun wrote: > > > I'd like to parse NCBI-Blast -m 3 option or -m 4 option. Is there any open > source programs for this?(C,Java or Perl) > > Thanks, > Eray > > > ERAY TUZUN, MS > Senior Computer Specialist > Department of Genome Sciences > University of Washington > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ------------------------------ _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board End of BiO_Bulletin_Board Digest, Vol 8, Issue 1 ************************************************ From marty.gollery at gmail.com Fri Jun 3 12:12:49 2005 From: marty.gollery at gmail.com (Martin Gollery) Date: Fri, 3 Jun 2005 09:12:49 -0700 Subject: [BiO BB] A database system for in-house sequence collections In-Reply-To: References: <20050603054637.5145333E62@smtp2.bgu.ac.il> Message-ID: Hi Vered, This depends on what the nature of the sequences are, and what data you want to record. StackPack and Ensemble are both very good, as Marcos has pointed out. If you want the system to keep track of additional information about the clones, vectors, sequencing conditions etc, then you might have a look at the MAGIC database system from the Pratt group at University of Georgia. MAGIC keeps track of all this information, which can be very useful when you have to go back to it years later. Check it out at: http://fungen.org/Laboratory/Bioinformatics.htm Marty On 6/3/05, Marcos Oliveira de Carvalho wrote: > > Hi Vered, > > I have tested and used Sabia (http://www.sabia.lncc.br/), GenDb > (http://www.cebitec.uni-bielefeld.de/groups/brf/software/gendb_info/) and > Manatee (http://manatee.sourceforge.net/) for microbial genome management > and annotation (all are good tools, I recommend that you try each and see > what fits better to your needs). For EST sequences I found StackPack > (http://www.sanbi.ac.za/CODES/STACKPACK_REQUEST/) very useful. If you are > looking systems for more complex genomes, you should try GMOD > (http://www.gmod.org/) and ENSEMBL (http://www.ensembl.org/) > > Cheers > > Marcos > > > > On Fri, 03 Jun 2005 05:03:00 -0300, Vered Caspi > wrote: > > > I am looking for a freely available software for storage (preferably in > > MySQL), management and batch analysis of collections of sequences and > > their annotations. The sequences are usually generated in-house by > > various research groups. > > We can currently allocate a single Linux server for this purpose. > > Any advice will be highly welcome. > > Vered > > > > === > > Vered Caspi, Ph.D. > > Bioinformatics Support Unit, Head > > National Institute for Biotechnology in the Negev, > > Building 39, room 214 > > Ben-Gurion University of the Negev > > Beer-Sheva 84105, Israel > > Email: veredcc at bgumail.bgu.ac.il > > Tel: 08-6479034 054-7915969 > > > > > > > > > > _______________________________________________ > > Bioinformatics.Org general forum - > > BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ----------- From magda_mansour at yahoo.fr Mon Jun 6 09:57:58 2005 From: magda_mansour at yahoo.fr (Magda Mansour) Date: Mon, 6 Jun 2005 15:57:58 +0200 (CEST) Subject: [BiO BB] NCBI-toolkit : import_project.sh / import_project.wsf on Linux In-Reply-To: Message-ID: <20050606135758.39681.qmail@web26801.mail.ukl.yahoo.com> Hello, I'm trying to work "independently in the C++ subtree" of the NCBI toolkit, but I can't find the import_project.sh script in the ncbi site as recommanded by the tutorial. There is only the import_project.wsf script which I can't run from Linux. (it gives me a permission denied message) Can I find this script somewhere else? Is there a special way for running the *.wsf on linux? (I didn't find any relevant info on Internet) Thank you for your help, Magda Mansour _____________________________________________________________________________ D?couvrez le nouveau Yahoo! Mail : 1 Go d'espace de stockage pour vos mails, photos et vid?os ! Cr?ez votre Yahoo! Mail sur http://fr.mail.yahoo.com From deepan_3356 at yahoo.co.in Tue Jun 7 16:05:19 2005 From: deepan_3356 at yahoo.co.in (deepan@bioinformatics.org) Date: Tue, 7 Jun 2005 21:05:19 +0100 (BST) Subject: [BiO BB] Automation of data mining. Message-ID: <20050607200519.36861.qmail@web8410.mail.in.yahoo.com> Dear all, I would like to bring before you a problem that i face in automation of a data mining process. I have to find the Km(Michaelis Menten Constants) for a set of ~2479 enzymatic reactions. I've got a list of the form: rxn id, rxn type(reversible/irrev), substrate ids, product ids, enzyme name. All these data were obtained from KEGG and so the ids mentioned are keggids and are not directly compatible with BRENDA. But Km values are available in BRENDA only. how do I do this. Plz keep in mind that, Km vales are specific for enzyme-reaction sets and not just for enzymes. Plz someone help me. I'm ready to restructure my list also if needed. Plz tell me how to automate this process. my home page http://deepan.tk mail id : deepan at bioinformatics.org ----------------------------------------- deepan chakravarthy n 3rd year,(5th sem), b.tech(biotech), center for biotechnology, anna university , chennai. ph no: home:04287-241199,04287-244399, brother no:9840824399, address: ac tech hostel (jh 108), anna university, chennai-25. ___________________________________________________________ Does your mail provider give you FREE antivirus protection? Get Yahoo! Mail http://uk.mail.yahoo.com From christoph.gille at charite.de Fri Jun 10 06:38:14 2005 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Fri, 10 Jun 2005 12:38:14 +0200 (CEST) Subject: [BiO BB] Need installation of Bio software on Mac Message-ID: <35532.192.168.220.204.1118399894.squirrel@webmail.charite.de> Hi everybody, If you have a Mac OSX I would like to ask you for help. Could you please test whether some new parts of the STRAP software also work properly under Macintosh. It takes only 5 min. The problem is that the new software is installed from source code and I do not know how Macintosh handles C/C++ programs. The idea behind is that though I do not have a Macintosh I would be able to provide new algorithms for Macintosh. Please launch STRAP with the webstart link http://www.charite.de/bioinf/strap/strap2.jnlp or click the webstart button on the home page http://www.charite.de/bioinf/strap/ Two new alignment programs are included: MUSCLE and DIALIGN-t and I do not know whether their installation works properly. To get to the alignment form you can follow the first three panels of the Tutorial which automatically comes up at start. Instead of CLUSTALW you select MUSCLE or DIALIGN-t. An automated installing process is started and "make" is run. I guess that Mac (though it is some sort of UNIX) has no C-compiler and probably this installation process will fail until Gnu C-compiler is installed. Is this difficult to install ? How do people install gcc? Can I initiate the installation process of gcc automatically from STRAP ? Is there a Web-Site for gcc ? Are there other C/C++ -compilers around ? A third program TOPPRED can predict transmembrane helices and plot hydrophobicity profiles and is accessed from the menu "predict" or "analyze/plot profile.. ." Many thanks Christoph From nix at bioroot.org Tue Jun 14 00:02:52 2005 From: nix at bioroot.org (David Nix) Date: Mon, 13 Jun 2005 21:02:52 -0700 Subject: [BiO BB] BioRoot Bioinformatics Message-ID: Hello Folks, I wanted to announce a free service for molecular biology labs. It's a web based bio reagent LIMS. http://bioroot.org/Documentation.jsp BioRoot is a non-profit organization dedicated to fostering communication, collaboration, and increased productivity in the biological sciences through information exchange. This is an open access initiative to bring new meaning to the phrase "clone by phone." Clone by Click? Do give the demo a try and let us know if you would like an account for your laboratory. Its free and will accelerate your research benefiting the scientist and ultimately the patient. David Nix, Executive Director From willy_valdivia at orionbiosciences.com Mon Jun 13 23:09:23 2005 From: willy_valdivia at orionbiosciences.com (willy_valdivia at orionbiosciences.com) Date: Mon, 13 Jun 2005 20:09:23 -0700 Subject: [BiO BB] Call for Papers: Virtual Conference on Genomics and Bioinformatics Message-ID: <20050614030923.14040.qmail@gem-wbe03.mesa1.secureserver.net> Please apologize multiple postings ************************************************************************************** Call for Papers: Fifth Virtual Conference on Genomics and Bioinformatics ************************************************************************************* http://www.virtualgenomics.org/vcgb/conference_2005.htm Submission Deadline: June 30, 2005 The Virtual Conference on Genomics and Bioinformatics provides an advanced collaborative environment where high profile researchers discuss the challenges and opportunities in the understanding of living systems. There are NO REGISTRATION FEES to participate in this event. The main objective of the Proceedings of the Virtual Conference is to establish a prestigious compilation of research advances, discussions and reviews on emerging issues related with genomics and bioinformatics. To attain maximum interaction among the authors and their readers, each submitted paper will subject to a stringent double blind review process, and accepted manuscripts will be invited for oral presentations and published both in paper and electronic forms. Topics covered by the 2005 Issue will include: Artificial and Synthetic Life Biological Knowledge Representation Biological Data Mining Data Visualization Educational Experiences and Policies Related to Genomics and Bioinformatics Evolutionary Genomics Genomic Data Standardization, Management, and Integration High Throughput and GRID Computing Machine Learning Techniques for Genomic Analysis Nano-biotechnology Proteomic Analysis Protein Structural Analysis and Modeling Systems Biology Structural Genomics A maximum length of four pages will be considered for publication as poster and twelve pages as a paper. All accepted manuscripts will be considered for publication in PLoS Computational Biology. From p.balaji at gmail.com Tue Jun 14 10:02:35 2005 From: p.balaji at gmail.com (Balaji) Date: Tue, 14 Jun 2005 19:32:35 +0530 Subject: [BiO BB] Problem with BLAST Message-ID: <881c0222050614070247b894ae@mail.gmail.com> Hi everyone, I have a protein that comprises only of Alanine(A), Glycine(G), Cysteine(C) and Threonine(T). When i try to use NCBI BLAST with this protein, the blast program returns an error saying that the entered sequence is a nucleotide (as it evidently has only A's, T's, C's and G's) and not a protein sequence. Is there anyway i work around the problem? I'll be grateful for any help Thanks in advance Balaji From landman at scalableinformatics.com Tue Jun 14 10:27:46 2005 From: landman at scalableinformatics.com (Joe Landman) Date: Tue, 14 Jun 2005 10:27:46 -0400 Subject: [BiO BB] Problem with BLAST In-Reply-To: <881c0222050614070247b894ae@mail.gmail.com> References: <881c0222050614070247b894ae@mail.gmail.com> Message-ID: <42AEE962.1010303@scalableinformatics.com> Did you mean to translate your nucleotide sequence into a protein sequence? You would need to use either blastx to do the translation, or one of the tblast series (depending upon what you were searching against). Balaji wrote: > Hi everyone, > I have a protein that comprises only of Alanine(A), Glycine(G), > Cysteine(C) and Threonine(T). When i try to use NCBI BLAST with this > protein, the blast program returns an error saying that the entered > sequence is a nucleotide (as it evidently has only A's, T's, C's and > G's) and not a protein sequence. > Is there anyway i work around the problem? I'll be grateful for any help > Thanks in advance > Balaji -- Joseph Landman, Ph.D Founder and CEO Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://www.scalableinformatics.com phone: +1 734 786 8423 fax : +1 734 786 8452 cell : +1 734 612 4615 From biopctgi at yahoo.es Tue Jun 14 10:57:43 2005 From: biopctgi at yahoo.es (Jose Maria Gonzalez Izarzugaza) Date: Tue, 14 Jun 2005 16:57:43 +0200 Subject: [BiO BB] Problem with BLAST In-Reply-To: <42AEE962.1010303@scalableinformatics.com> References: <881c0222050614070247b894ae@mail.gmail.com> <42AEE962.1010303@scalableinformatics.com> Message-ID: <42AEF067.6080703@yahoo.es> The fact is that BLAST counts the percentage of [ATCG] in the query or something similar. You can try a query like that ATATACACATTTGArrrrrrr setting the option 'Mask lower case' to active. It works (or seems to) and returns an aligment for the ATATAT...GA zone... by chance???... Maybe. :o( Good luck! Txema Joe Landman wrote: > Did you mean to translate your nucleotide sequence into a protein > sequence? You would need to use either blastx to do the translation, > or one of the tblast series (depending upon what you were searching > against). > > Balaji wrote: > >> Hi everyone, >> I have a protein that comprises only of Alanine(A), Glycine(G), >> Cysteine(C) and Threonine(T). When i try to use NCBI BLAST with this >> protein, the blast program returns an error saying that the entered >> sequence is a nucleotide (as it evidently has only A's, T's, C's and >> G's) and not a protein sequence. >> Is there anyway i work around the problem? I'll be grateful for >> any help >> Thanks in advance >> Balaji > > > From operon at cbiot.ufrgs.br Tue Jun 14 11:10:15 2005 From: operon at cbiot.ufrgs.br (Marcos Oliveira de Carvalho) Date: Tue, 14 Jun 2005 12:10:15 -0300 Subject: [BiO BB] Problem with BLAST In-Reply-To: <881c0222050614070247b894ae@mail.gmail.com> References: <881c0222050614070247b894ae@mail.gmail.com> Message-ID: I think that you hit a bug of BLAST(p). Either the manual or "blastall" do not show a way to deal with that problem. Maybe the way BLAST know if the sequence is protein or DNA is hardcoded, like clustal (using the symbol frequencies). One trick could be change the symbols of your protein (A by W, G by L, ...) and modify the score matrix you are using accordingly. cheers Marcos On Tue, 14 Jun 2005 11:02:35 -0300, Balaji wrote: > Hi everyone, > I have a protein that comprises only of Alanine(A), Glycine(G), > Cysteine(C) and Threonine(T). When i try to use NCBI BLAST with this > protein, the blast program returns an error saying that the entered > sequence is a nucleotide (as it evidently has only A's, T's, C's and > G's) and not a protein sequence. > Is there anyway i work around the problem? I'll be grateful for any > help > Thanks in advance > Balaji > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From cortig at free.fr Tue Jun 14 12:23:29 2005 From: cortig at free.fr (Corentin =?iso-8859-1?Q?Cras=2DM=E9neur?=) Date: Tue, 14 Jun 2005 11:23:29 -0500 Subject: [BiO BB] Need installation of Bio software on Mac In-Reply-To: <35532.192.168.220.204.1118399894.squirrel@webmail.charite.de> References: <35532.192.168.220.204.1118399894.squirrel@webmail.charite.de> Message-ID: ? 12:38 +0200 le 06/10/05, Dr. Christoph Gille a ?crit: > >Instead of CLUSTALW you select MUSCLE or DIALIGN-t. An automated >installing process is started and "make" is run. > >I guess that Mac (though it is some sort of UNIX) has no C-compiler >and probably this installation process will fail until Gnu C-compiler >is installed. I have gcc 3 and 4 on my Mac (Part of X-Code 2.1 on MacOS X 10.4). When I tried to install DIALIGN-t, the app downloaded the sources then warned me that it had failed to launch dialign-t. The same warning asked me to copy the dialign-t.exe binary to a specific location on my drive. If I take the precompiled binaries available on the dialign-t website and place them where Strap asks em to, I still get the same error warning if I try to align using dialign-t (a problem with the name of the binary that sure doesn't have the .exe ??) Corentin PS: I also noticed that your app installs the java version of CLUSTALW instead of using the regular compiled binaries which are much much faster. It actually doesn't even tries to launch CLUSTALW on the Mac. I have it installed in /usr/local/bin (which is in my $PATH) but Strap still downloaded and built the Java version. From idoerg at burnham.org Tue Jun 14 14:19:45 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Tue, 14 Jun 2005 11:19:45 -0700 Subject: [BiO BB] Postdoc: evolutionary bioinformatics in Lausanne Message-ID: <42AF1FC1.5050605@burnham.org> A post-doctoral fellowship will be available in October 2005 to join a new lab of Evolutionary Bioinformatics at Lausanne University (Switzerland). There is no predefined subject, but the post-doc should fit in the general topics of the lab, namely the evolution of gene and genome function in animals. The work can be more biological or more methodological. I am open to any good CV from biology, bioinformatics or computer science, but some knowledge of programming and some knowledge of biology is a prerequisite. If you are interested, please send to marc at sdsc.edu your CV, email and phone contact information of two references, and a one page research project. More information here: http://www.sdsc.edu/~marc/lausanne.html Marc ____ Marc Robinson-Rechavi marc at sdsc.edu http://www.sdsc.edu/~marc Joint Center for Structural Genomics write to: Godzik lab, Burnham Institute, 10901 North Torrey Pines road, La Jolla, CA 92037, USA phone: +1 858 646 3100 x3553; fax: +1 858 713 9949 La liberte ne s'use que quand on ne s'en sert pas From jeff at bioinformatics.org Tue Jun 14 18:39:27 2005 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 14 Jun 2005 18:39:27 -0400 Subject: [BiO BB] [Fwd: ENC plot] Message-ID: <42AF5C9F.8050102@bioinformatics.org> An embedded message was scrubbed... From: Subhash Agarwal Subject: ENC plot Date: Tue, 14 Jun 2005 06:37:37 +0100 (BST) Size: 2283 URL: From christoph.gille at charite.de Wed Jun 15 04:14:16 2005 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Wed, 15 Jun 2005 10:14:16 +0200 (CEST) Subject: [BiO BB] Need installation of Bio software on Mac In-Reply-To: References: <35532.192.168.220.204.1118399894.squirrel@webmail.charite.de> Message-ID: <43336.192.168.220.204.1118823256.squirrel@webmail.charite.de> Dear Corentin, many thanks for taking the time to try this out. I generally append the suffix dot exe to binaries because this allows me to have the same documentation for DOS and UNIX. A symbolic link (ln -s ...) of the clustalW or dialign-t binarie to the specified directory is only recognized when it gets the ending dot exe. Most binaries like clustalW come in an JAR archive because some require more than one file. Even though the clustalW version is the ordinary C-version and not a java-version. I am a bit disappointed that the installation of dialign-t fails on Mac. Theroetically, STRAP should go to the directory $HOME/charite.christo.settings/bin/dialign-t/ Subsequently the command make should be executed finally the binary should be renamed mv dialign-t dialign-t.exe Do you know which of these steps failed ? Supposed it would work, how do you like the concept of distributing the source rather than executables ? Best regards Christoph > ? 12:38 +0200 le 06/10/05, Dr. Christoph Gille a ?crit: > >> >> Instead of CLUSTALW you select MUSCLE or DIALIGN-t. An automated >> installing process is started and "make" is run. >> >> I guess that Mac (though it is some sort of UNIX) has no C-compiler >> and probably this installation process will fail until Gnu C-compiler is >> installed. > > I have gcc 3 and 4 on my Mac (Part of X-Code 2.1 > on MacOS X 10.4). When I tried to install DIALIGN-t, the app downloaded the > sources then warned me that it had failed to launch dialign-t. The same > warning asked me to copy the dialign-t.exe binary to a specific location > on my drive. > > If I take the precompiled binaries available on > the dialign-t website and place them where Strap asks em to, I still get > the same error warning if I try to align using dialign-t (a problem with > the name of the binary that sure doesn't have the .exe ??) > > > Corentin > > > > PS: I also noticed that your app installs the > java version of CLUSTALW instead of using the regular compiled binaries > which are much much faster. It actually doesn't even tries to launch > CLUSTALW on the Mac. I have it installed in > /usr/local/bin (which is in my $PATH) but Strap > still downloaded and built the Java version. > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From golharam at umdnj.edu Tue Jun 14 15:43:21 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Tue, 14 Jun 2005 15:43:21 -0400 Subject: [BiO BB] Mapping Accession # to cytogenetic position Message-ID: <000a01c57119$51effa90$e6028a0a@GOLHARMOBILE1> Does anyone know how I can map an accession # to the gene's cytogenetic position? I need a way to do this for a bunch of accession #'s, preferrably an automated way... Ryan From cortig at free.fr Wed Jun 15 19:38:49 2005 From: cortig at free.fr (Corentin =?iso-8859-1?Q?Cras=2DM=E9neur?=) Date: Wed, 15 Jun 2005 18:38:49 -0500 Subject: [BiO BB] Need installation of Bio software on Mac In-Reply-To: <43336.192.168.220.204.1118823256.squirrel@webmail.charite.de> References: <35532.192.168.220.204.1118399894.squirrel@webmail.charite.de> <43336.192.168.220.204.1118823256.squirrel@webmail.charite.de> Message-ID: ? 10:14 +0200 le 06/15/05, Dr. Christoph Gille a ?crit: >Dear Corentin, Hi Christoph, >many thanks for taking the time to try this out. Not a problem. >I generally append the suffix dot exe to binaries because this allows me >to have the same documentation for DOS and UNIX. I see. >A symbolic link (ln -s ...) of the clustalW or dialign-t binarie to the >specified directory is only recognized when it gets the ending dot exe. >Most binaries like clustalW come in an JAR archive because some require >more than one file. Even though the clustalW version is the ordinary >C-version and not a java-version. Very true too (though you can have a system to detect the platform and adapt the symlinks accordingly, but I get your point). I still believe it could be worth querying the system to check whether the apps are not already installed somewhere else (eg: /usr/local/bin), but I realize it represents more work for you. > >I am a bit disappointed that the installation of dialign-t fails on Mac. > >Theroetically, STRAP should go to the directory >$HOME/charite.christo.settings/bin/dialign-t/ > >Subsequently the command make >should be executed > >finally the binary should be renamed >mv dialign-t dialign-t.exe > > >Do you know which of these steps failed ? The console reports: >2005-06-15 18:19:02.536 java[692] tabletProximity: >FocusManager noResponderFor called >2005-06-15 18:19:18.955 java[692] tabletProximity: >Jun 15 18:19:31 Corentin java[695]: tabletProximity: >Jun 15 18:21:26 Corentin java[695]: tabletProximity: The .jar file was properly downloaded and the dialign-t folder contains all the source files. I (very briefly) saw a warning that mentioned make (but it was too fast nor me to actually read it). If I move to this directory and run make I get: >gcc -O3 -march=i686 -funroll-loops -c -o museq.o museq.c >cc1: error: invalid option 'arch=i686' >make: *** [museq.o] Error 1 If I rename Makefile.MAC_OS into Makefile and run make, I get the binary. I can then rename it and use it in the app. I used it on the example sequences and all I got was "no score availabel" (with the same typo). Since I know almost nothing about dialign-t, that might as well have been expected. >Supposed it would work, how do you like the concept of distributing the >source rather than executables ? It's a tough choice. Binaries are convenient and allow deployment regardless of the fact that people have installed gcc. Distributing the sources instead would require that people have installed X-Code on their Mac (which should be the case for most people running command-line applications for bioinformatics anyway). I tend to like the sources better... Don't hesitate to ping me off-list if you need additional information and don;t want to bother the rest of the list. Corentin From cortig at free.fr Wed Jun 15 19:42:34 2005 From: cortig at free.fr (Corentin =?iso-8859-1?Q?Cras=2DM=E9neur?=) Date: Wed, 15 Jun 2005 18:42:34 -0500 Subject: [BiO BB] Need installation of Bio software on Mac In-Reply-To: <43336.192.168.220.204.1118823256.squirrel@webmail.charite.de> References: <35532.192.168.220.204.1118399894.squirrel@webmail.charite.de> <43336.192.168.220.204.1118823256.squirrel@webmail.charite.de> Message-ID: ? 10:14 +0200 le 06/15/05, Dr. Christoph Gille a ?crit: >Do you know which of these steps failed ? Similar problem for Muscle. Make gives me this error: >g++ -c -O3 -march=pentiumpro -mcpu=pentiumpro >-funroll-loops -Winline -DNDEBUG=1 >aligngivenpath.cpp -o aligngivenpath.o >cc1plus: error: invalid option 'arch=pentiumpro' >aligngivenpath.cpp:1: error: bad value (pentiumpro) for -mcpu= switch >make: *** [aligngivenpath.o] Error 1 Again, the makefile is not adapted for MacOS: No "Pentium Pro" option for us... (yet :-> ). Corentin From nuraini at cs.usm.my Wed Jun 15 22:11:07 2005 From: nuraini at cs.usm.my (Nur'Aini Abdul Rashid) Date: Thu, 16 Jun 2005 10:11:07 +0800 Subject: [BiO BB] Patterns Message-ID: <000e01c57218$ab1c3020$8482cf0a@MyBox2> Can multiple patterns(motif??) of a protein represents same structure or function. if it does do a dictionary of this knowledge exist? Nur'Aini binti Abdul Rashid Pusat Pengajian Sains Komputer Universiti Sains Malaysia Pulau Pinang. -------------- next part -------------- An HTML attachment was scrubbed... URL: From felipe.albrecht at gmail.com Thu Jun 16 08:37:04 2005 From: felipe.albrecht at gmail.com (Felipe Albrecht) Date: Thu, 16 Jun 2005 09:37:04 -0300 Subject: [BiO BB] Patterns In-Reply-To: <000e01c57218$ab1c3020$8482cf0a@MyBox2> References: <000e01c57218$ab1c3020$8482cf0a@MyBox2> Message-ID: Yes, a structure can be represented by varius motifs. A motif represents a structure, but a structure dont nescessaly represents only one motif. Exist some docs about this, but now I dont know. Felipe Albrecht 2005/6/15, Nur'Aini Abdul Rashid : > > Can multiple patterns(motif??) of a protein represents same structure or > function. if it does do a dictionary of this knowledge exist? > > > Nur'Aini binti Abdul Rashid > Pusat Pengajian Sains Komputer > Universiti Sains Malaysia > Pulau Pinang. > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > From nuraini at cs.usm.my Thu Jun 16 22:00:31 2005 From: nuraini at cs.usm.my (Nur'Aini Abdul Rashid) Date: Fri, 17 Jun 2005 10:00:31 +0800 Subject: [BiO BB] Patterns References: <000e01c57218$ab1c3020$8482cf0a@MyBox2> Message-ID: <001e01c572e0$5b255060$8482cf0a@MyBox2> Thank you... how do I go about searching the aticles... any tips... ----- Original Message ----- From: "Felipe Albrecht" To: "The general forum at Bioinformatics.Org" Sent: Thursday, June 16, 2005 8:37 PM Subject: Re: [BiO BB] Patterns > Yes, a structure can be represented by varius motifs. > > A motif represents a structure, but a structure dont nescessaly > represents only one motif. Exist some docs about this, but now I dont > know. > > Felipe Albrecht > > 2005/6/15, Nur'Aini Abdul Rashid : >> >> Can multiple patterns(motif??) of a protein represents same structure or >> function. if it does do a dictionary of this knowledge exist? >> >> >> Nur'Aini binti Abdul Rashid >> Pusat Pengajian Sains Komputer >> Universiti Sains Malaysia >> Pulau Pinang. >> _______________________________________________ >> Bioinformatics.Org general forum - >> BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> >> > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From lray at albany.edu Fri Jun 17 13:09:05 2005 From: lray at albany.edu (Lipika Ray) Date: Fri, 17 Jun 2005 13:09:05 -0400 (EDT) Subject: [BiO BB] (no subject) Message-ID: <1692.169.226.137.250.1119028145.squirrel@169.226.137.250> Hi, I have accession numbers of interferon and also sequences. I just want to know whether this protein have any crystal structure or not. Also structure related information (like other homologous proteins ...) about this protein. How should I proceed? Thanking you, Lipika Ray ++++++++++++++++++++++++++++++++++++ Dr. Lipika Ray Postdoctoral Researcher SUNY, UAlbany From idoerg at burnham.org Fri Jun 17 13:31:54 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Fri, 17 Jun 2005 10:31:54 -0700 Subject: [BiO BB] Patterns In-Reply-To: <001e01c572e0$5b255060$8482cf0a@MyBox2> References: <000e01c57218$ab1c3020$8482cf0a@MyBox2> <001e01c572e0$5b255060$8482cf0a@MyBox2> Message-ID: <42B3090A.5020206@burnham.org> Sound like you might need a textbook first. http://bioinformatics.org/faq/#books The Chapter 10 in David Mount's book is a good start. There are several motif databases, but using them depends on what you call a "motif", and what is your actual goal is. Anything within the range of PRINTS, BLOCKS, Pfam, PROSITE, 3D-motif and I-SITES can be applied to your question, at some level. You might also want to look at this page: http://us.expasy.org/tools/#pattern HTH, Iddo Nur'Aini Abdul Rashid wrote: > Thank you... how do I go about searching the aticles... any tips... > > > > ----- Original Message ----- From: "Felipe Albrecht" > > To: "The general forum at Bioinformatics.Org" > > Sent: Thursday, June 16, 2005 8:37 PM > Subject: Re: [BiO BB] Patterns > > >> Yes, a structure can be represented by varius motifs. >> >> A motif represents a structure, but a structure dont nescessaly >> represents only one motif. Exist some docs about this, but now I dont >> know. >> >> Felipe Albrecht >> >> 2005/6/15, Nur'Aini Abdul Rashid : >> >>> >>> Can multiple patterns(motif??) of a protein represents same >>> structure or >>> function. if it does do a dictionary of this knowledge exist? >>> >>> >>> Nur'Aini binti Abdul Rashid >>> Pusat Pengajian Sains Komputer >>> Universiti Sains Malaysia >>> Pulau Pinang. >>> _______________________________________________ >>> Bioinformatics.Org general forum - >>> BiO_Bulletin_Board at bioinformatics.org >>> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >>> >>> >>> >> _______________________________________________ >> Bioinformatics.Org general forum - >> BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> > > _______________________________________________ > Bioinformatics.Org general forum - > 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 9949 http://ffas.ljcrf.edu/~iddo ========================== The First Automated Protein Function Prediction SIG Detroit, MI June 24, 2005 http://ffas.burnham.org/AFP From marty.gollery at gmail.com Fri Jun 17 13:38:58 2005 From: marty.gollery at gmail.com (Martin Gollery) Date: Fri, 17 Jun 2005 10:38:58 -0700 Subject: [BiO BB] (no subject) In-Reply-To: <1692.169.226.137.250.1119028145.squirrel@169.226.137.250> References: <1692.169.226.137.250.1119028145.squirrel@169.226.137.250> Message-ID: The structure of Interferon-g has been solved- see http://sgce.cbse.uab.edu/carson/papers/ifn/ifn.html Marty On 6/17/05, Lipika Ray wrote: > Hi, > > I have accession numbers of interferon and also sequences. I just want to > know whether this protein have any crystal structure or not. Also > structure related information (like other homologous proteins ...) about > this protein. How should I proceed? > > Thanking you, > > Lipika Ray > > ++++++++++++++++++++++++++++++++++++ > Dr. Lipika Ray > Postdoctoral Researcher > SUNY, UAlbany > > > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ----------- From dmb at mrc-dunn.cam.ac.uk Fri Jun 17 13:42:50 2005 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 17 Jun 2005 18:42:50 +0100 (BST) Subject: [BiO BB] (no subject) In-Reply-To: <1692.169.226.137.250.1119028145.squirrel@169.226.137.250> Message-ID: On Fri, 17 Jun 2005, Lipika Ray wrote: >Hi, > >I have accession numbers of interferon and also sequences. I just want to >know whether this protein have any crystal structure or not. Also >structure related information (like other homologous proteins ...) about >this protein. How should I proceed? Here is one way to go... http://pdbbeta.rcsb.org/pdb/search/searchSequence.do > >Thanking you, > >Lipika Ray > >++++++++++++++++++++++++++++++++++++ >Dr. Lipika Ray >Postdoctoral Researcher >SUNY, UAlbany > > > > >_______________________________________________ >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From yezhiqiang at gmail.com Fri Jun 17 13:49:24 2005 From: yezhiqiang at gmail.com (yezhiqiang at gmail.com) Date: Sat, 18 Jun 2005 01:49:24 +0800 Subject: [BiO BB] Is there a good way to find orthologue sequences? Message-ID: <34198fe4050617104945cffc72@mail.gmail.com> Dear all, Is there a good way to find orthologue sequences? I mean, I have a protein sequence in species A, how could I get all the available corresponding sequences from other species? I blast my sequence to nr, there are just too many hits with low e-value and high identity, so that some "corresponding" sequences from distant related species could not be find by blast. Is there any good method for automatically solve this problem? Thank you very much. From christoph.gille at charite.de Fri Jun 17 15:12:34 2005 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Fri, 17 Jun 2005 21:12:34 +0200 (CEST) Subject: [BiO BB] Is there a good way to find orthologue sequences? In-Reply-To: <34198fe4050617104945cffc72@mail.gmail.com> References: <34198fe4050617104945cffc72@mail.gmail.com> Message-ID: <52926.192.168.220.204.1119035554.squirrel@webmail.charite.de> There is always the danger of picking a paralogous sequence instead. If two genes are orthologous then the sequence identity should be typical for the two species. If they are paralogous the sequence identiy is higher. I am not convinced that this can be solved completely automatically. Christoph > Dear all, > Is there a good way to find orthologue sequences? I mean, I have a > protein sequence in species A, how could I get all the available > corresponding sequences from other species? I blast my sequence to nr, > there are just too many hits with low e-value and high identity, so that > some "corresponding" sequences from distant related species could not be > find by blast. Is there any good method for automatically solve this > problem? > > Thank you very much. > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From christoph.gille at charite.de Fri Jun 17 15:17:07 2005 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Fri, 17 Jun 2005 21:17:07 +0200 (CEST) Subject: [BiO BB] (no subject) In-Reply-To: <1692.169.226.137.250.1119028145.squirrel@169.226.137.250> References: <1692.169.226.137.250.1119028145.squirrel@169.226.137.250> Message-ID: <44460.192.168.220.204.1119035827.squirrel@webmail.charite.de> Many blast services allow to search against the pdb-sequences. "http://www.ebi.ac.uk/blast2/", "http://www.expasy.org/tools/blast/", "http://www.ncbi.nlm.nih.gov", Best regards Christoph > Hi, > > > I have accession numbers of interferon and also sequences. I just want to > know whether this protein have any crystal structure or not. Also > structure related information (like other homologous proteins ...) about > this protein. How should I proceed? > > Thanking you, > > > Lipika Ray > > > ++++++++++++++++++++++++++++++++++++ > Dr. Lipika Ray > Postdoctoral Researcher > SUNY, UAlbany > > > > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From sariego9 at yahoo.com Fri Jun 17 16:04:01 2005 From: sariego9 at yahoo.com (Diego Martinez) Date: Fri, 17 Jun 2005 13:04:01 -0700 (PDT) Subject: [BiO BB] Is there a good way to find orthologue sequences? In-Reply-To: <52926.192.168.220.204.1119035554.squirrel@webmail.charite.de> Message-ID: <20050617200401.19353.qmail@web32507.mail.mud.yahoo.com> commonly the only way one will use the term orthologous is if you are using all the genes of 2 genomes. The reasoning goes like this: for gene A in genome 1, and for gene B in genome 2, if the highest scoring hit to gene A from genome B is gene 2, and if the highest scoring hit to gene 2 from genome A is gene 1, then gene 1 and gene 2 are potential orthologs. I hope I said that right. This is called either bi-directional best hits or mutual best hits. It might be easier to draw out also. Most researchers I know who deal with this sort of thing conclude that without the entire genome, you can not really be sure that you are looking at a true ortholog, it could be a "co-ortholog" or as Christoph said, a paralog. Also see Overbeek et al (PNAS v.96(6); Mar 16, 1999) Diego --- "Dr. Christoph Gille" wrote: > There is always the danger of picking a paralogous sequence instead. > If two genes are orthologous then the sequence identity should be > typical for the two species. > If they are paralogous the sequence identiy is higher. > I am not convinced that this can be solved completely automatically. > > Christoph > > > > > > Dear all, > > Is there a good way to find orthologue sequences? I mean, I have a > > protein sequence in species A, how could I get all the available > > corresponding sequences from other species? I blast my sequence to nr, > > there are just too many hits with low e-value and high identity, so that > > some "corresponding" sequences from distant related species could not be > > find by blast. Is there any good method for automatically solve this > > problem? > > > > Thank you very much. > > _______________________________________________ > > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .=$=. .=$=. .=$=. .=$=. .=$=. .=$=. @ @ | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | @ @ | ~' `~$~' `~$~' `~$~' `~$~' `~$~' `~ __________________________________ Discover Yahoo! Find restaurants, movies, travel and more fun for the weekend. Check it out! http://discover.yahoo.com/weekend.html From operon at cbiot.ufrgs.br Fri Jun 17 17:34:17 2005 From: operon at cbiot.ufrgs.br (Marcos Oliveira de Carvalho) Date: Fri, 17 Jun 2005 18:34:17 -0300 Subject: [BiO BB] Is there a good way to find orthologue sequences? In-Reply-To: <20050617200401.19353.qmail@web32507.mail.mud.yahoo.com> References: <20050617200401.19353.qmail@web32507.mail.mud.yahoo.com> Message-ID: Another good discussion about orthology and paralogy can be found here: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12446146&dopt=Abstract And Lerat et al, presents a novel approach for determining orthology in: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12975657&query_hl=4 Marcos On Fri, 17 Jun 2005 17:04:01 -0300, Diego Martinez wrote: > commonly the only way one will use the term > orthologous is if you are using all the genes > of 2 genomes. The reasoning goes like this: > for gene A in genome 1, and for gene B in > genome 2, if the highest scoring hit to gene A > from genome B is gene 2, and if the highest > scoring hit to gene 2 from genome A is gene > 1, then gene 1 and gene 2 are potential > orthologs. I hope I said that right. > This is called either bi-directional > best hits or mutual best hits. It might > be easier to draw out also. > Most researchers I know who deal with > this sort of thing conclude that without the > entire genome, you can not really > be sure that you are looking at a true > ortholog, it could be a "co-ortholog" > or as Christoph said, a paralog. > Also see Overbeek et al (PNAS v.96(6); Mar 16, 1999) > > Diego > > --- "Dr. Christoph Gille" wrote: > >> There is always the danger of picking a paralogous sequence instead. >> If two genes are orthologous then the sequence identity should be >> typical for the two species. >> If they are paralogous the sequence identiy is higher. >> I am not convinced that this can be solved completely automatically. >> >> Christoph >> >> >> >> >> > Dear all, >> > Is there a good way to find orthologue sequences? I mean, I have a >> > protein sequence in species A, how could I get all the available >> > corresponding sequences from other species? I blast my sequence to >> nr, >> > there are just too many hits with low e-value and high identity, so >> that >> > some "corresponding" sequences from distant related species could not >> be >> > find by blast. Is there any good method for automatically solve this >> > problem? >> > >> > Thank you very much. >> > _______________________________________________ >> > Bioinformatics.Org general forum - >> BiO_Bulletin_Board at bioinformatics.org >> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> > >> > >> >> >> _______________________________________________ >> Bioinformatics.Org general forum - >> BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > .=$=. .=$=. .=$=. .=$=. .=$=. > .=$=. > @ @ | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | > | > | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | > | > | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | @ @ > | > ~' `~$~' `~$~' `~$~' `~$~' `~$~' > `~ > > > > __________________________________ > Discover Yahoo! > Find restaurants, movies, travel and more fun for the weekend. Check it > out! > http://discover.yahoo.com/weekend.html > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From virajj at lycos.com Fri Jun 17 18:56:59 2005 From: virajj at lycos.com (vijaya raj) Date: Fri, 17 Jun 2005 17:56:59 -0500 Subject: [BiO BB] (no subject) Message-ID: <20050617225659.77B0FE5BC7@ws7-2.us4.outblaze.com> hi if you want to use ur accession number to search for structure... try structure database in ncbi. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=structure you might as well want to use "interferon" as the key word against NCBI structure database. you might also try a NCBI blastp against pdb database. goodluk vijayaraj nagarajan department of biological sciences the university of southern mississippi MS USA ----- Original Message ----- From: "Lipika Ray" To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] (no subject) Date: Fri, 17 Jun 2005 13:09:05 -0400 (EDT) > > Hi, > > I have accession numbers of interferon and also sequences. I just want to > know whether this protein have any crystal structure or not. Also > structure related information (like other homologous proteins ...) about > this protein. How should I proceed? > > Thanking you, > > Lipika Ray > > ++++++++++++++++++++++++++++++++++++ > Dr. Lipika Ray > Postdoctoral Researcher > SUNY, UAlbany > > > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- _______________________________________________ NEW! Lycos Dating Search. The only place to search multiple dating sites at once. http://datingsearch.lycos.com From yezhiqiang at gmail.com Sat Jun 18 05:11:15 2005 From: yezhiqiang at gmail.com (yezhiqiang at gmail.com) Date: Sat, 18 Jun 2005 17:11:15 +0800 Subject: [BiO BB] Is there a good way to find orthologue sequences? In-Reply-To: References: <20050617200401.19353.qmail@web32507.mail.mud.yahoo.com> Message-ID: <34198fe405061802114222184@mail.gmail.com> Thank you all for these good suggestions and help for clear my conceptions about ortholog and paralog. 2005/6/18, Marcos Oliveira de Carvalho : > > Another good discussion about orthology and paralogy can be found here: > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12446146&dopt=Abstract > > And Lerat et al, presents a novel approach for determining orthology in: > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12975657&query_hl=4 > > Marcos > > On Fri, 17 Jun 2005 17:04:01 -0300, Diego Martinez > wrote: > > > commonly the only way one will use the term > > orthologous is if you are using all the genes > > of 2 genomes. The reasoning goes like this: > > for gene A in genome 1, and for gene B in > > genome 2, if the highest scoring hit to gene A > > from genome B is gene 2, and if the highest > > scoring hit to gene 2 from genome A is gene > > 1, then gene 1 and gene 2 are potential > > orthologs. I hope I said that right. > > This is called either bi-directional > > best hits or mutual best hits. It might > > be easier to draw out also. > > Most researchers I know who deal with > > this sort of thing conclude that without the > > entire genome, you can not really > > be sure that you are looking at a true > > ortholog, it could be a "co-ortholog" > > or as Christoph said, a paralog. > > Also see Overbeek et al (PNAS v.96(6); Mar 16, 1999) > > > > Diego > > > > --- "Dr. Christoph Gille" wrote: > > > >> There is always the danger of picking a paralogous sequence instead. > >> If two genes are orthologous then the sequence identity should be > >> typical for the two species. > >> If they are paralogous the sequence identiy is higher. > >> I am not convinced that this can be solved completely automatically. > >> > >> Christoph > >> > >> > >> From lray at albany.edu Fri Jun 17 12:10:54 2005 From: lray at albany.edu (Lipika Ray) Date: Fri, 17 Jun 2005 12:10:54 -0400 (EDT) Subject: [BiO BB] (no subject) Message-ID: <1601.169.226.137.250.1119024654.squirrel@169.226.137.250> Hi, I have accession numbers of interferon and also sequences. I just want to know whether this protein have any crystal structure or not. Also structure related information (like other homologous proteins ...) about this protein. How should I proceed? Thanking you, Lipika Ray ++++++++++++++++++++++++++++++++++++ Dr. Lipika Ray Postdoctoral Researcher SUNY, UAlbany From cortig at free.fr Fri Jun 17 15:16:08 2005 From: cortig at free.fr (Corentin =?iso-8859-1?Q?Cras=2DM=E9neur?=) Date: Fri, 17 Jun 2005 14:16:08 -0500 Subject: [BiO BB] Is there a good way to find orthologue sequences? In-Reply-To: <34198fe4050617104945cffc72@mail.gmail.com> References: <34198fe4050617104945cffc72@mail.gmail.com> Message-ID: ? 01:49 +0800 le 06/18/05, a ?crit: >Dear all, > Is there a good way to find orthologue sequences? I mean, I have a >protein sequence in species A, how could I get all the available >corresponding sequences from other species? I blast my sequence to >nr, there are just too many hits with low e-value and high identity, >so that some "corresponding" sequences from distant related species >could not be find by blast. Is there any good method for automatically >solve this problem? You can always download Homologene from the NCBI. If you have the Unigene or LocusLink IDs for your genes, you can easily find the already annotated orthologs through Homologene. It's all on the FTP server of the NCBI if I quite remember. Corentin From etlevy at ucsd.edu Fri Jun 17 19:31:00 2005 From: etlevy at ucsd.edu (Levy, Essy) Date: Fri, 17 Jun 2005 16:31:00 -0700 Subject: [BiO BB] Systems Biology and Bioengineering Short Program Message-ID: <44CEA569398B4748AFE5488144201821E18795@ono-exchange.AD.UCSD.EDU> Dear Bioinformatics.org, Bellow you will find information on an upcoming course to take place at UCSD Extension, on July 6-8, 2005 I have also attached a PDF file with the same information: If you have any questions or concerns please feel free to contact me. Thank you, Essy Systems Biology & Bioengineering July 6-8, 2005 Gain an advanced understanding of the cutting-edge field of Systems Biology! Dr. Bernhard Palsson, renowned scientist and professor of Bioengineering at UCSD, partners with UCSD Extension's Bioscience Department to present this 3-day intensive course focused on helping current university faculty, life-science researchers, and others gain an advanced understanding of the cutting-edge field of systems biology. Through the combination of lecture and lab based instruction, participants will explore the molecular- and engineering-levels of biology and gain a thorough understanding of the developments in this new field. The course focuses on: * Reconstructing biochemical reaction networks using heterogeneous data sources * Characterizing the topological properties of the reconstructed networks * Determining the functional states of networks and how to compare computation with experimental results The program includes: * The various high-throughput data types, how they are generated, and interpreted * The heterogeneous high-throughput data types and how they are used to reconstruct cellular reaction networks * The representation of network reconstructions as chemically and genetically structured databases * The way to mathematically represent reconstructed networks * The capabilities and properties of networks and how they are analyzed * Analyzing the structural, steady state and dynamic properties of networks * The public and commercial software packages are used for such analysis Date/Time: July 6-8, 2005 8:00 a.m.-5:00 p.m. Location: UCSD Extension, Sorrento Mesa Center Cingular Wireless Building Room 112 6925 Lusk Blvd. San Diego, CA 92121 Fee: $1195 (Includes continental breakfast, lunch, and course materials.) Bernhard Palsson, Ph.D., is a Professor of Bioengineering and Adjunct Professor Medicine at UCSD. He is an inventor of over 20 U.S. patents, many of which are in the area of hematopoietic stem cell transplantation, bioreactor design, gene transfer, high-throughput single cell manipulation, network reconstruction, in silico model building and metabolic engineering. He is the founder/co-founder of: AASTROM BIOSCIENCES, ONCOSIS, CYNTELLECT, GENOMATICA, and the Iceland Genomics Corporation. Information: Call Essy Levy at (858)-622-5736 or e-mail etlevy at ucsd.edu. To enroll: Call (858)-534-3400 or visit www.extension.ucsd.edu/registration. Section ID #: 051129 Essy Levy M.S. Bioscience Programs Coordinator UCSD Extension Bioscience 858-622-5736 etlevy at ucsd.edu http://bioscience.ucsd.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Systems Bio.pdf Type: application/octet-stream Size: 185667 bytes Desc: Systems Bio.pdf URL: From virajj at lycos.com Sun Jun 19 01:13:02 2005 From: virajj at lycos.com (vijaya raj) Date: Sun, 19 Jun 2005 00:13:02 -0500 Subject: [BiO BB] graph-theory-software Message-ID: <20050619051302.3BA263384B@ws7-3.us4.outblaze.com> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From idoerg at burnham.org Sun Jun 19 02:02:15 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Sat, 18 Jun 2005 23:02:15 -0700 Subject: [BiO BB] graph-theory-software In-Reply-To: <20050619051302.3BA263384B@ws7-3.us4.outblaze.com> Message-ID: GraphViz might be what you are looking for. It will mot take a binary matrix file as input (well, there is no real standard for those) but you can easily convert to GraphViz readable files. Their syntax is very simple. http://www.graphviz.org HTH, 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) 646 3171 http://ffas.ljcrf.edu/~iddo ------------------------------------- Automated Protein Function Prediction Meeting, June 24, 2005 http://ffas.burnham.org/AFP On Sun, 19 Jun 2005, vijaya raj wrote: > hi > i have a binary matrix file, representing a biological network. > is there any graph theory software that would allow me to draw the network, taking the binary matrix file as the input... > > thanks in advance for sparing your time. > > vijayaraj nagarajan > department of biological sciences > the university of southern mississippi > ms, usa > > > -- > _______________________________________________ > NEW! Lycos Dating Search. The only place to search multiple dating sites at once. > http://datingsearch.lycos.com > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From dmb at mrc-dunn.cam.ac.uk Sun Jun 19 06:33:42 2005 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Sun, 19 Jun 2005 11:33:42 +0100 (BST) Subject: [BiO BB] graph-theory-software In-Reply-To: Message-ID: On Sat, 18 Jun 2005, Iddo Friedberg wrote: >GraphViz might be what you are looking for. It will mot take a binary >matrix file as input (well, there is no real standard for those) but you >can easily convert to GraphViz readable files. Their syntax is very >simple. > >http://www.graphviz.org My favourite is JUNG (Java Universal Network and Graph Archetecture), but again you probably have to change your graph format. > >HTH, > >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) 646 3171 >http://ffas.ljcrf.edu/~iddo >------------------------------------- >Automated Protein Function Prediction Meeting, June 24, 2005 >http://ffas.burnham.org/AFP > >On Sun, 19 Jun 2005, vijaya raj wrote: > >> hi >> i have a binary matrix file, representing a biological network. >> is there any graph theory software that would allow me to draw the network, taking the binary matrix file as the input... >> >> thanks in advance for sparing your time. >> >> vijayaraj nagarajan >> department of biological sciences >> the university of southern mississippi >> ms, usa >> >> >> -- >> _______________________________________________ >> NEW! Lycos Dating Search. The only place to search multiple dating sites at once. >> http://datingsearch.lycos.com >> >> _______________________________________________ >> Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> > >_______________________________________________ >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From boris.steipe at utoronto.ca Sun Jun 19 09:37:01 2005 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Sun, 19 Jun 2005 09:37:01 -0400 Subject: [BiO BB] graph-theory-software In-Reply-To: Message-ID: <372280BE-E0C7-11D9-8357-000A9577512E@utoronto.ca> Many people working with biological networks use cytoscape. http://www.cytoscape.org/ B. On Sunday, Jun 19, 2005, at 06:33 America/Montreal, Dan Bolser wrote: > > My favourite is JUNG (Java Universal Network and Graph Archetecture), > but > again you probably have to change your graph format. > > On Sat, 18 Jun 2005, Iddo Friedberg wrote: > >> GraphViz might be what you are looking for. It will mot take a binary >> matrix file as input (well, there is no real standard for those) but >> you >> can easily convert to GraphViz readable files. Their syntax is very >> simple. >> >> http://www.graphviz.org >> >> HTH, >> >> 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) 646 3171 >> http://ffas.ljcrf.edu/~iddo >> ------------------------------------- >> Automated Protein Function Prediction Meeting, June 24, 2005 >> http://ffas.burnham.org/AFP >> >> On Sun, 19 Jun 2005, vijaya raj wrote: >> >>> hi >>> i have a binary matrix file, representing a biological network. >>> is there any graph theory software that would allow me to draw the >>> network, taking the binary matrix file as the input... >>> >>> thanks in advance for sparing your time. >>> >>> vijayaraj nagarajan >>> department of biological sciences >>> the university of southern mississippi >>> ms, usa From lray at albany.edu Sun Jun 19 19:36:00 2005 From: lray at albany.edu (Lipika Ray) Date: Sun, 19 Jun 2005 19:36:00 -0400 (EDT) Subject: [BiO BB] Re: searching-for-interferon-structures Message-ID: <1137.24.194.183.39.1119224160.squirrel@24.194.183.39> Hi, Many many thanks for your reply. Actually I want to find the structure of Interferon alpha 2b, alpha 5a and a GFP protein. For Interferon alpha 2b I just followed the method you have said, structure database in ncbi and I found a crystal structure for that. But for the other two, I have accession numbers and nucleotide sequence. So how will I know about the structure of protein from that nucleotide sequence? Thanking you in advance. Lipika Ray ++++++++++++++++++++++++++++++++++++++++++ Dr. Lipika Ray Postdoctoral researcher SUNY, UAlbany > hey.. > didnt u get the replies sent through the board...? > wel if not..let me repeat... > 1. you can choose ncbi accession number, to search ncbi structure database. > 2. you can use ncbi blastp to search against pdb database, using sequence. 3. you can also go to pdb website to execute a sequence based query. > > atleast one of these should work. > goodluk. > > vijayaraj nagarajan > department of biological sciences > the university of southern mississippi > ms, usa > > -- > _______________________________________________ > NEW! Lycos Dating Search. The only place to search multiple dating sites at once. > http://datingsearch.lycos.com > > From golharam at umdnj.edu Mon Jun 20 00:13:38 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Mon, 20 Jun 2005 00:13:38 -0400 Subject: [BiO BB] Is there a good way to find orthologue sequences? In-Reply-To: <34198fe4050617104945cffc72@mail.gmail.com> Message-ID: <001c01c5754e$70810650$b800a8c0@GOLHARMOBILE1> Take a look at the following references. They all put together ways of finding orthologous sequences. I'm using the database Ouyang constructed. Lee, Y., R. Sultana, et al. (2002). "Cross-Referencing Eukaryotic Genomes: TIGR Orthologous Gene Alignments (TOGA)." Genome Res. 12(3): 493-502. Mushegian, A. R., J. R. Garey, et al. (1998). "Large-Scale Taxonomic Profiling of Eukaryotic Model Organisms: A Comparison of Orthologous Proteins Encoded by the Human, Fly, Nematode, and Yeast?Genomes." Genome Res. 8(6): 590-598. Ouyang, M., J. Case, et al. (2003). "Five Hundred Sixty-Five Triples of Chicken, Human, and Mouse Candidate Orthologs." Journal of Molcular Evolution 57(3): 271-281. ----- Ryan Golhar Computational Biologist The Informatics Institute at The University of Medicine & Dentistry of NJ Phone: 973-972-5034 Fax: 973-972-7412 Email: golharam at umdnj.edu -----Original Message----- From: bio_bulletin_board-bounces+ryangolhar=hotmail.com at bioinformatics.org [mailto:bio_bulletin_board-bounces+ryangolhar=hotmail.com at bioinformatics .org] On Behalf Of yezhiqiang at gmail.com Sent: Friday, June 17, 2005 1:49 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Is there a good way to find orthologue sequences? Dear all, Is there a good way to find orthologue sequences? I mean, I have a protein sequence in species A, how could I get all the available corresponding sequences from other species? I blast my sequence to nr, there are just too many hits with low e-value and high identity, so that some "corresponding" sequences from distant related species could not be find by blast. Is there any good method for automatically solve this problem? Thank you very much. _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From henry.lenzi at gmail.com Sun Jun 19 01:22:58 2005 From: henry.lenzi at gmail.com (Henry Lenzi) Date: Sun, 19 Jun 2005 02:22:58 -0300 Subject: [BiO BB] graph-theory-software In-Reply-To: <20050619051302.3BA263384B@ws7-3.us4.outblaze.com> References: <20050619051302.3BA263384B@ws7-3.us4.outblaze.com> Message-ID: <8b4c81f0506182222edfaf14@mail.gmail.com> http://www.graphviz.org/About.php On 6/19/05, vijaya raj wrote: > hi > i have a binary matrix file, representing a biological network. > is there any graph theory software that would allow me to draw the network, taking the binary matrix file as the input... > > thanks in advance for sparing your time. > > vijayaraj nagarajan > department of biological sciences > the university of southern mississippi > ms, usa > > > -- > _______________________________________________ > NEW! Lycos Dating Search. The only place to search multiple dating sites at once. > http://datingsearch.lycos.com > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From virajj at lycos.com Mon Jun 20 09:38:12 2005 From: virajj at lycos.com (vijaya raj) Date: Mon, 20 Jun 2005 08:38:12 -0500 Subject: [BiO BB] graph-theory-software Message-ID: <20050620133812.A8E47E5BC7@ws7-2.us4.outblaze.com> my sincere thanks to Iddo,Dan,Boris,Henry and others for your valuable suggestions on graph theory-software. vijayaraj nagarajan department of biological sciences the university of southern mississippi ms, usa ----- Original Message ----- From: "Henry Lenzi" To: "The general forum at Bioinformatics.Org" Subject: Re: [BiO BB] graph-theory-software Date: Sun, 19 Jun 2005 02:22:58 -0300 > > http://www.graphviz.org/About.php > > On 6/19/05, vijaya raj wrote: > > hi > > i have a binary matrix file, representing a biological network. > > is there any graph theory software that would allow me to draw > > the network, taking the binary matrix file as the input... > > > > thanks in advance for sparing your time. > > > > vijayaraj nagarajan > > department of biological sciences > > the university of southern mississippi > > ms, usa > > > > > > -- > > _______________________________________________ > > NEW! Lycos Dating Search. The only place to search multiple > > dating sites at once. > > http://datingsearch.lycos.com > > > > _______________________________________________ > > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- _______________________________________________ NEW! Lycos Dating Search. The only place to search multiple dating sites at once. http://datingsearch.lycos.com From vxg189 at bham.ac.uk Mon Jun 20 10:08:53 2005 From: vxg189 at bham.ac.uk (Vibhor Gupta) Date: Mon, 20 Jun 2005 15:08:53 +0100 Subject: [BiO BB] Determining non-coding regions in a DNA sequence Message-ID: <1B4C5BA3CB5F2849B0C8DB99156046A43AC532@med-ex1.bham.ac.uk> Hello, Is there a program that could determine the non-coding regions (and other elements such as repeat elements, coding regions etc) that are present within a given DNA sequence. Thanking you all. Mr. Vibhor Gupta Research Associate (Chromatin and Gene Expression Group) Division of Immunity and Infection - Anatomy Institute of Biomedical Research University of Birmingham Birmingham - B15 2TT Email: v.gupta.1 at bham.ac.uk Telephone number: 0121-4158684 From jon.rees at bioinformaticsforumuk.net Mon Jun 20 09:04:18 2005 From: jon.rees at bioinformaticsforumuk.net (Jon Rees) Date: Mon, 20 Jun 2005 14:04:18 +0100 Subject: [BiO BB] Call for Abstracts - Young Bioinformaticians Forum Message-ID: <01e901c57598$916ff700$277549a1@acs.brookes.ac.uk> ================================== Young Bioinformaticians Forum 2005 ================================== *** Call for Abstracts *** 21st October 2005 at the Institute of Physics, London, UK ======================= Meeting Venue and Times ======================= YBF 2005 will be held at the prestigious Institute of Physics, 76 Portland Place, London W1B 1NT, UK. The conference opens on Friday October 21st, 2005 at 09:15h and closes at 17.00h. On the 21st of October 2005, the and UK Bioinformatics Forum (UKBF, http://www.bio.org.uk), RSC Molecular Modelling Group (MMG, http://www.rscmodelling.org/) and the Institute of Physics (http://www.iop.org/) will jointly hold the third annual Young Bioinformaticians Forum 2005 (YBF). BMC Bioinformatics is the media partner for this meeting. The web site for the meeting, which contains links to all last year?s talks, is: http://www.ybf.org The winning speaker will receive a prize of ?250, and the winning poster will win ?100. Last year?s meeting was a tremendous success, with over 130 attendees. Like last year, the purpose of the YBF is two-fold: (i) YBF is an opportunity for postgraduates to present research among their peer group in a competitive but friendly atmosphere (ii) YBF is a networking opportunity for post-docs, group leaders and industry to seek out new talent and keep abreast of fast moving topics ================== Call for Abstracts ================== We are calling for abstracts and posters in the following areas of bioinformatics: * Systems Biology * Structural biology * Genome analysis and annotation * Data mining * Computational biology * Ontologies We aim to attract the best pre-PhD bioinformaticians to speak and attend the YBF from as wide an area of bioinformatics as possible. YBF is inclusive, being open to applications from current post-graduate students of all ages, from all universities and all countries. If you are a postgraduate student, I should like to invite you to submit an abstract. If you are a supervisor, I should like to invite you to nominate a graduate student to speak at the meeting, who should then submit an abstract. =================== Abstract submission =================== Please submit abstract by Aug 15th 2005 to be considered to as a speaker, or September 15th 2005 to be considered for a poster presentation. Those delegates whose abstracts were not selected for speaking slots will automatically be considered for a poster presentation. The organizers will sift through submitted abstracts and select a balanced and appropriate agenda from these submissions. Each abstract should include the surnames and initials of the authors, as well as a title, the affiliatons of the authors (University or Institute Department of School), the abstract (text only) should be no more than 300 words. ================ Registration Fee ================ The registration fee for students is just ?50 (?58.75 inc. VAT before Sept. 21, ?75 after Sept 21 - ?88.13 inc. VAT), for academics, postdocs and industry scientists registration is ?85 (?99.88 inc. VAT before Sept. 21, ?115 after Sept 21 - ?135.13 inc. VAT). This includes refreshments upon arrival, lunch and coffee breaks. Click here to register: http://www.ybf.org/registration.htm =========== Sponsorship =========== If your organisation might wish to consider sponsoring the meeting, or bring an exhibition stand, please take a look at the available options - http://www.ybf.org/sponsorship.html UK Bioinformatics Forum is a non-profit ISCB associated regional group which will act as an advocate and society for UK bioinformatics: Terms of Reference - http://www.bioinformaticsforumuk.net/menu.php?nav=menu/L2EJKE5PAD Contact: ybf at bioinformaticsforumuk.net Best Wishes Dr Jon Rees (Project Manager) on behalf of UK Bioinformatics Forum Dr Darren Flower, Dr Derek Gatherer, Dr Charlotte Deane (YBF Organisers) Oxford OX3 0BP United Kingdom Tel. +44 (0) 1865 484224 Mob. +44 (0) 7970 893371 Fax. +44 (0) 1865 484478 http://www.ybf.org/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From Sudhindra.Gadagkar at notes.udayton.edu Mon Jun 20 10:54:36 2005 From: Sudhindra.Gadagkar at notes.udayton.edu (Sudhindra.Gadagkar at notes.udayton.edu) Date: Mon, 20 Jun 2005 10:54:36 -0400 Subject: [BiO BB] Determining non-coding regions in a DNA sequence In-Reply-To: <1B4C5BA3CB5F2849B0C8DB99156046A43AC532@med-ex1.bham.ac.uk> Message-ID: Vibhor, There may be others, but I know GrailExp (http://compbio.ornl.gov/grailexp/) does what you are looking for. And it's free. Good luck, Sudhindra Gadagkar ---------------------------------------------------------------------------- Sudhindra R. Gadagkar, Ph.D. Department of Biology University of Dayton 300 College Park Dayton, OH 45469-2320 Ph: (937) 229-2410 Fax: (937) 229-2021 Email: gadagkar at notes.udayton.edu ---------------------------------------------------------------------------- "Vibhor Gupta" Sent by: bio_bulletin_board-bounces+gadagkar=notes.udayton.edu at bioinformatics.org 06/20/2005 10:08 AM Please respond to "The general forum at Bioinformatics.Org" To cc Subject [BiO BB] Determining non-coding regions in a DNA sequence Hello, Is there a program that could determine the non-coding regions (and other elements such as repeat elements, coding regions etc) that are present within a given DNA sequence. Thanking you all. Mr. Vibhor Gupta Research Associate (Chromatin and Gene Expression Group) Division of Immunity and Infection - Anatomy Institute of Biomedical Research University of Birmingham Birmingham - B15 2TT Email: v.gupta.1 at bham.ac.uk Telephone number: 0121-4158684 _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From v.moreno at ico.scs.es Tue Jun 21 12:50:26 2005 From: v.moreno at ico.scs.es (Moreno Aguado, Victor) Date: Tue, 21 Jun 2005 18:50:26 +0200 Subject: [BiO BB] course on proteomics Message-ID: <5FF3F11444E3A9439191AA1EDCB69A1721C6F9@icosrvmail01.ICO.SCS.local> Hi, I send info on this course that might be of your interest Victor --------------------------------------------------------- Course on STATISTICAL ANALYSIS OF PROTEOMICS DATA finding proteomic biomarkers for diagnosis and prognosis with Mass Spectrometry Barcelona, September 14th-16th 2005 Lecturer Prof. Yutaka Yasui Department of Public Health Sciences Faculty of Medicine and Dentistry University of Alberta Organizer Dr. Victor Moreno Bioinformatics and Biostatistics Unit Cancer Epidemiology and Registry Department Catalan Institute of Oncology. Course language All the lectures will be given in English. Aim Advances in mass spectrometry over the last few years have led to a revolution in the field of proteomics. This course will cover all the issues involved in mass spectrometry data analysis, from raw data to final discovery of protein biomarkers and classification of samples according to their protein pattern. Short preliminary program: 1. Brief introduction to biology, genomics and proteomics. 2. Introduction to mass spectrometry (MS). 3. MS data preprocessing and experimental design. 4. Analysis of single peaks as biomarkers. 5. Defining proteomic patterns: building and testing predictors with MS data. Course details http://lbe.uab.es/proteomics From lray at albany.edu Wed Jun 22 10:29:00 2005 From: lray at albany.edu (Lipika Ray) Date: Wed, 22 Jun 2005 10:29:00 -0400 (EDT) Subject: [BiO BB] Protease binding site prediction software Message-ID: <2655.169.226.137.250.1119450540.squirrel@169.226.137.250> Hi, I just want to know is there any software available freely for prediction of protease binding site with a given primary sequence of a protein? Thanking you, Lipika Ray +++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. Lipika RAy Postdoctoral researcher SUNY, UAlbany From idoerg at burnham.org Wed Jun 22 12:11:00 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed, 22 Jun 2005 09:11:00 -0700 Subject: [BiO BB] Protease binding site prediction software In-Reply-To: <2655.169.226.137.250.1119450540.squirrel@169.226.137.250> Message-ID: http://pops.csse.monash.edu.au/index.html -- 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) 646 3171 http://ffas.ljcrf.edu/~iddo ------------------------------------- Automated Protein Function Prediction Meeting, June 24, 2005 http://ffas.burnham.org/AFP On Wed, 22 Jun 2005, Lipika Ray wrote: > Hi, > > I just want to know is there any software available freely for prediction > of protease binding site with a given primary sequence of a protein? > Thanking you, > > Lipika Ray > > +++++++++++++++++++++++++++++++++++++++++++++++++++ > Dr. Lipika RAy > Postdoctoral researcher > SUNY, UAlbany > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From lray at albany.edu Wed Jun 22 12:42:03 2005 From: lray at albany.edu (Lipika Ray) Date: Wed, 22 Jun 2005 12:42:03 -0400 (EDT) Subject: [BiO BB] Protease binding site prediction software In-Reply-To: References: <2655.169.226.137.250.1119450540.squirrel@169.226.137.250> Message-ID: <1875.169.226.137.250.1119458523.squirrel@169.226.137.250> Hi Iddo, Thanks for your link. But I want to find chloroplast protease binding site in a given primary sequence. PoPS is in different format. Thanking you. Lipika > > http://pops.csse.monash.edu.au/index.html > > -- > 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) 646 3171 > http://ffas.ljcrf.edu/~iddo > ------------------------------------- > Automated Protein Function Prediction Meeting, June 24, 2005 > http://ffas.burnham.org/AFP > > On Wed, 22 Jun 2005, Lipika Ray wrote: > >> Hi, >> >> I just want to know is there any software available freely for >> prediction >> of protease binding site with a given primary sequence of a protein? >> Thanking you, >> >> Lipika Ray >> >> +++++++++++++++++++++++++++++++++++++++++++++++++++ >> Dr. Lipika RAy >> Postdoctoral researcher >> SUNY, UAlbany >> >> _______________________________________________ >> Bioinformatics.Org general forum - >> BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> > > From ada at bionet.nsc.ru Wed Jun 22 03:57:02 2005 From: ada at bionet.nsc.ru (Dmitry Afonnikov) Date: Wed, 22 Jun 2005 14:57:02 +0700 Subject: [BiO BB] BGRS'2005 Summer School "Evolution, Systems Biology and High Performance Computing Bioinformatics" Message-ID: The International School of Young Scientist "Evolution, Systems Biology and High Performance Computing Bioinformatics", Novosibirsk, September 11-16, 2005 INFORMATIONAL LETTER Dear Colleagues! The International School of Young Scientist "Evolution, Systems Biology and High Performance Computing Bioinformatics" will be held under the auspicies of the BGRS (Bioinformatics of the Genome Regulation and Structure) conference at Academgorodok, September 11-16, 2005. The conference is organized by the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences and is supported by the Russian Foundation for Basic Research. It will be an interdisciplinary workshop concerned with the application of supercomputer technologies to the problems of evolutionary and systems biology. It will be a continuation of the lines of scientific inquiry followed in the preceding BGRS conferences at Akademgorodok. Leading Scientists in Russia and outside it will be involved as professionals in the promotion of parallel computing applications to modern biological problems, such as phylogenetic tree building, modeling of nucleotide and amino acid sequence evolution, integrative or systems biology. The Summer School WWW-site: http://www.bionet.nsc.ru/meeting/bgrs_school/ E-mail address: bgrs_school at bionet.nsc.ru Registration and abstract submission. To participate in the School, registration at the Summer School WWW-site is needed before August 1, 2005 (for foreign participants) Additional information is available at the Summer School WWW-site. Organizing Commettee address: 10, Lavrentyev Ave., Institute of Cytology and Genetics SB RAS, Novosibirsk, 634090, Russia. Dmitry Afonnikov Tel.: (3832) 33-29-71 Fax.: (3832) 33-12-78 From willy_valdivia at orionbiosciences.com Wed Jun 22 14:48:59 2005 From: willy_valdivia at orionbiosciences.com (willy_valdivia at orionbiosciences.com) Date: Wed, 22 Jun 2005 11:48:59 -0700 Subject: [BiO BB] Virtual Conference: Call for Papers Message-ID: <20050622184859.775.qmail@webmail10.mesa1.secureserver.net> Please apologize multiple postings ************************************************************************************** Call for Papers: Fifth Virtual Conference on Genomics and Bioinformatics ************************************************************************************** Send your article to: papers at virtualgenomics.org ************************************************************************************** http://www.virtualgenomics.org/vcgb/conference_2005.htm Submission Deadline: June 30, 2005 The main objective of the Proceedings of the Virtual Conference is to establish a prestigious compilation and open access of research advances, discussions and reviews on emerging issues related with genomics and bioinformatics. To attain maximum interaction among the authors and their readers, each submitted paper will subject to a stringent double blind review process, and accepted manuscripts will be invited for oral presentations and published both in paper and electronic forms. Topics covered by the 2005 Issue will include: Artificial and Synthetic Life Biological Knowledge Representation Biological Data Mining Data Visualization Educational Experiences and Policies Related to Genomics and Bioinformatics Evolutionary Genomics Genomic Data Standardization, Management, and Integration High Throughput and GRID Computing Machine Learning Techniques for Genomic Analysis Nanobiotechnology Proteomic Analysis Protein Structural Analysis and Modeling Systems Biology Structural Genomics Format instructions: http://www.virtualgenomics.org/vcgb/papers_2005.htm From elavv2003 at gmail.com Tue Jun 21 22:43:41 2005 From: elavv2003 at gmail.com (Elavazhagan) Date: Wed, 22 Jun 2005 08:13:41 +0530 Subject: [BiO BB] Re: BiO_Bulletin_Board Digest, Vol 8, Issue 16 In-Reply-To: <20050621160043.28D05D20FF@www.bioinformatics.org> References: <20050621160043.28D05D20FF@www.bioinformatics.org> Message-ID: Hai U can determine using any exon prediction tools like Glimmer,Genescan,genemark,hmmgene etc.As well as u can use some of the ORF finder tool that has been maintained in ncbi (http://www.ncbi.nlm.nih.gov/projects/gorf/).From that u can easily split the genome sequence into CDS and non coding regions(introns). I think still it has not been predicted the exat functions of introns and why do them exist in genome. Bye. On 6/21/05, bio_bulletin_board-request at bioinformatics.org wrote: > Send BiO_Bulletin_Board mailing list submissions to > bio_bulletin_board at bioinformatics.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > or, via email, send a message with subject or body 'help' to > bio_bulletin_board-request at bioinformatics.org > > You can reach the person managing the list at > bio_bulletin_board-owner at bioinformatics.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of BiO_Bulletin_Board digest..." > > > Today's Topics: > > 1. Re: Determining non-coding regions in a DNA sequence > (Sudhindra.Gadagkar at notes.udayton.edu) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 20 Jun 2005 10:54:36 -0400 > From: Sudhindra.Gadagkar at notes.udayton.edu > Subject: Re: [BiO BB] Determining non-coding regions in a DNA sequence > To: "The general forum at Bioinformatics.Org" > > Message-ID: > > > Content-Type: text/plain; charset="us-ascii" > > Vibhor, > > There may be others, but I know GrailExp > (http://compbio.ornl.gov/grailexp/) does what you are looking for. And > it's free. > > Good luck, > > Sudhindra Gadagkar > > ---------------------------------------------------------------------------- > Sudhindra R. Gadagkar, Ph.D. > Department of Biology > University of Dayton > 300 College Park > Dayton, OH 45469-2320 > > Ph: (937) 229-2410 > Fax: (937) 229-2021 > Email: gadagkar at notes.udayton.edu > ---------------------------------------------------------------------------- > > > > > "Vibhor Gupta" > Sent by: > bio_bulletin_board-bounces+gadagkar=notes.udayton.edu at bioinformatics.org > 06/20/2005 10:08 AM > Please respond to > "The general forum at Bioinformatics.Org" > > > > To > > cc > > Subject > [BiO BB] Determining non-coding regions in a DNA sequence > > > > > > > Hello, > > Is there a program that could determine the non-coding regions (and other > elements such as repeat elements, coding regions etc) that are present > within a given DNA sequence. Thanking you all. > > Mr. Vibhor Gupta > Research Associate (Chromatin and Gene Expression Group) > Division of Immunity and Infection - Anatomy > Institute of Biomedical Research > University of Birmingham > Birmingham - B15 2TT > Email: v.gupta.1 at bham.ac.uk > Telephone number: 0121-4158684 > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://bioinformatics.org/pipermail/bio_bulletin_board/attachments/20050620/fe26c089/attachment-0001.htm > > ------------------------------ > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > End of BiO_Bulletin_Board Digest, Vol 8, Issue 16 > ************************************************* > -- E.Elavazhagan 09444332083 From rajat at isical.ac.in Thu Jun 23 01:00:10 2005 From: rajat at isical.ac.in (Rajat K. De) Date: Thu, 23 Jun 2005 10:30:10 +0530 Subject: [BiO BB] Research Position Message-ID: <42BA41DA.1040002@isical.ac.in> Dear Colleagues, I am enclosing below an advertisement for a Research Position for a project titled "Computational Analysis of Biochemical Pathways Related to Gene-activity and Metabolism" at the Indian Statistical Institute, Kolkata. Interested persons may apply in the prescribed format. Please forward this mail to the persons who may be interested. Regards, Rajat K. De Assistant Professor Machine Intelligence Unit Indian Statistical Institute 203 B. T. Road Kolkata 700108. E-mail: rajat at isical.ac.in ---------------------------------------------------------------------------------------------------------------------------------------------------------- INDIAN STATISTICAL INSTITUTE 203 Barrackpore Trunk Road Kolkata-700 108 ADVERTISEMENT No.: PU/507/ADV/C 457 Date : 14 June 2005 Applications are invited for two Project Linked Personnel (on purely temporary basis) in the Machine Intelligence Unit, to work in (one for each of) the following projects of the Institute. Name of the Projects: 1. Computational analysis of biochemical pathways related to gene-activity and metabolism. 2. Integration of spline and neural network methodologies for multiresolution classification. Qualifications: Essential - M.Sc. in Statistics/Mathematics/Biophysics/Bioinformatics/ Electronics/Computer Science or MCA, with good knowledge in Computer Programming. OR B.E./B.Tech. or equivalent in Computer Science, Electrical Engineering, Electronics, Information Technology with good knowledge in Computer Programming. Desirable: For Project No. 1, knowledge in Molecular Biology/Biochemistry. For Project No. 2, ME/M.Tech. or equivalent in Computer Science, Electrical Engineering, Electronics, Information Technology. Pay: Consolidated Rs. 11,000/- (Rupees eleven thousand only) to Rs. 13,000/- (Rupees thirteen thousand only) per month depending on the qualification and experience. Age: The age limit is 35 years as on April 1, 2005, with usual relaxation for SC/ST/OBC and Physically Handicapped candidates. Age relaxation may be given to outstanding candidates or candidates with relevant experience. Tenure of Appointment: The appointment will be made till 31st March 2006 which may be extended further depending upon the (i) requirement of the project (ii) availability of funds and (iii) performance of the candidate. Applications addressed to the Director of the Institute must include Name, Father?s Name, Address, E-mail, Phone, Date of Birth, Academic Qualifications (with percentage of marks obtained in each examination), Experience, if any, along with attested copies of all documents/testimonials, and should reach the Head, Machine Intelligence Unit, Indian Statistical Institute, 203, B.T . Road, Kolkata-700108, India, by June 30, 2005. The Institute reserves the right not to appoint any of the above. (K.B. Sinha) Director ----------------------------------------------------------------------------------------------------------------------------------------- From nuraini at cs.usm.my Thu Jun 23 03:57:45 2005 From: nuraini at cs.usm.my (Nur'Aini Abdul Rashid) Date: Thu, 23 Jun 2005 15:57:45 +0800 Subject: [BiO BB] Download data. Message-ID: <000e01c577c9$40f7a330$8482cf0a@MyBox2> Can anyone name me a site where I can to download protein families that were created based on sequence similarity, nuraini -------------- next part -------------- An HTML attachment was scrubbed... URL: From idoerg at burnham.org Thu Jun 23 09:17:42 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Thu, 23 Jun 2005 09:17:42 -0400 Subject: [BiO BB] Download data. In-Reply-To: <000e01c577c9$40f7a330$8482cf0a@MyBox2> References: <000e01c577c9$40f7a330$8482cf0a@MyBox2> Message-ID: <42BAB676.4010109@burnham.org> There are quite a few of those. Pfam is probably the default choice for most people. http://www.sanger.ac.uk/Software/Pfam/ Nur'Aini Abdul Rashid wrote: > Can anyone name me a site where I can to download protein families > that were created based on sequence similarity, > > > > nuraini > >------------------------------------------------------------------------ > >_______________________________________________ >Bioinformatics.Org general forum - 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 Tel: (858) 646 3100 x3516 Fax: (858) 713 9930 http://ffas.ljcrf.edu/~iddo From lxyiwc at yahoo.com Fri Jun 24 11:12:33 2005 From: lxyiwc at yahoo.com (l x yi) Date: Fri, 24 Jun 2005 08:12:33 -0700 (PDT) Subject: [BiO BB] profile search Message-ID: <20050624151233.34569.qmail@web31104.mail.mud.yahoo.com> Hi everyone, Does anyone know any software that does profile (weight matrix) search? In this case, the input is the weight matrix, and the pgm would search through databank such as swissprot to find related sequences? Thank you! Lily --------------------------------- Yahoo! Mail Stay connected, organized, and protected. Take the tour -------------- next part -------------- An HTML attachment was scrubbed... URL: From pmr at ebi.ac.uk Fri Jun 24 16:29:14 2005 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Fri, 24 Jun 2005 21:29:14 +0100 (BST) Subject: [BiO BB] profile search In-Reply-To: <20050624151233.34569.qmail@web31104.mail.mud.yahoo.com> References: <20050624151233.34569.qmail@web31104.mail.mud.yahoo.com> Message-ID: <1706.12.27.2.2.1119644954.squirrel@webmail.ebi.ac.uk> Lily (l x yi) writes: > Does anyone know any software that does profile (weight matrix) search? In > this case, the input is the weight matrix, and the pgm would search > through databank such as swissprot to find related sequences? EMBOSS includes the "profit" program to do this. The profile/weight matrix can be generated with the EMBOSS "prophecy" program or produced in a compatible format by other programs. The EMBOSS home page is http://emboss.sourceforge.net/ Hope this helps, Peter Rice From penghanchuan at yahoo.com Fri Jun 24 17:50:15 2005 From: penghanchuan at yahoo.com (Hanchuan Peng) Date: Fri, 24 Jun 2005 14:50:15 -0700 (PDT) Subject: [BiO BB] Call for Attendance: BioImage Data Mining and Informatics, Stanford, CA. Aug 12, 2005 Message-ID: <20050624215015.94368.qmail@web32903.mail.mud.yahoo.com> (Apologize if you receive multiple copies of this message from various mailing lists.) =============================== Call for Attendance International Workshop on BioImage Data Mining and Informatics Stanford University, California August 12, 2005 For the first time, the Life Sciences Society is sponsoring a unique forum to discuss the recent advances in informatics and data mining for cellular, molecular, and other biological and biomedical images. This workshop is a satellite event of the 2005 IEEE Computational Systems Bioinformatics conference, August 8-11, Stanford, CA. We invite you to attend this exciting event and be stimulated by experts of bioimage mining! With the development of advanced imaging techniques, the number of biological images acquired in digital form is growing rapidly. Large-scale bioimage databases are becoming available. Analysis of these images is shedding light on a great number of biological problems. The goal of this workshop is to bring together an interdisciplinary group of researchers to identify problems and present answers to bioimage data mining and informatics. With 4 sessions and 16 presentations in this one-day event, researchers from leading institutions will discuss a wide spectrum of topics related to bioimaging, image analysis and mining, databases and visualization, and how these technologies help to tackle biological problems. Attendees will learn the state-of-the-art technical information in this quickly growing field and gain insight into what the future holds. It will all happen August 12 on the beautiful campus of Stanford University. Check the following web sites for more information: Program - http://lifesciencessociety.org/Workshop/BIprogrm.html Registration - http://lifesciencessociety.org/Workshop/register.html Register today, space is limited! From lifei03 at gmail.com Sun Jun 26 04:18:46 2005 From: lifei03 at gmail.com (Frank Lee) Date: Sun, 26 Jun 2005 16:18:46 +0800 Subject: [BiO BB] difference between Refseq and Uniprot Message-ID: <42BE64E6.7020903@gmail.com> Hi, all, Recently, I am working on the protein sequence analysis. I found the Refseq is very different from Uniprot. Uniprot contains much more proteins if TrEMBL is included. Can any experts give some comments on these two protein database. Which one is more reliable? It seems Swiss is of the best quality, then Refseq, then TrEMBL. And also, It seems there are redundancy in Uniprot. Is that so? -Frank From DMUTANTZ at aol.com Sun Jun 26 13:27:35 2005 From: DMUTANTZ at aol.com (DMUTANTZ at aol.com) Date: Sun, 26 Jun 2005 13:27:35 EDT Subject: [BiO BB] problem with LWP::Simple Message-ID: <127.5efbe770.2ff03f87@aol.com> Hello I would be garteful for any help with this. I want to pull an id number (UniProt protein accession number) from a file using a regex. This works OK. I then wanted to use the number as part of a url to pull the relevant page back , so I could parse some information about the protein from the page. The code is very basic. My perl script: #!/usr/bin/perl # A script to pull out an id number from a file using a regex. #The id number(s0 are put into an array @accnumber. #The file I read in is html_test2.txt (attached to this mail). #Then use the id number as part of a url to get and store a webpage. #In this case to simplify things I just want to take the first #element of the @accnumber array and use that in the url use LWP::Simple; $a = 0; #ask for the file name print "please enter file name", "\n"; #open and read the file $filename1 = <>; open fileone, "$filename1" or die; while (!eof(fileone)) { my $line = ; if ( $line =~/UNIPROT:?\w+\s(\w{6})\s/) { @accnumber[$a]= $1."\n"; $a++; } } close fileone; $query_number = @accnumber[0]; #as a sanity check I print the number to STDOUT print $query_number; #I call the subroutine to return the webpage get_page($query_number); sub get_page { my $address = $_[0]; my $url = 'http://www.ebi.uniprot.org/uniprot-srv/xmlView.do?proteinId=' .$address .'_ORYSA&pager.offset=0'; my $html_file = 'page.html'; my $status = getstore($url, $html_file); die "No _URL::Error_ (:Error) " unless is_success($status); } exit; and the text file I parse to get my regex: BLASTP 2.0MP-WashU [13-Dec-2004] [decunix5.0a-ev6-IP32LF64 2004-12-15T17:03:39] Copyright (C) 1996-2004 Washington University, Saint Louis, Missouri USA. All Rights Reserved. Reference: Gish, W. (1996-2004) _http://blast.wustl.edu_ (http://blast.wustl.edu) Query= 24061 17154533 emb|CAC80823.1 (AJ251791) putative IAA1 protein [Oryza sativa] 1e-130 235 236 99.5% top hit (237 letters; record 1) Database: uniprot 1,880,849 sequences; 604,459,357 total letters. Searching....10....20....30....40....50....60....70....80....90....100% done Smallest Sum High Probability Sequences producing High-scoring Segment Pairs: Score P(N) N UNIPROT:Q75KX3_ORYSA Q84PD9 Putative auxin-responsive pro... 1203 1.2e-121 1 All Rights Reserved. Reference: Gish, W. (1996-2004) Thanks for any help. -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanielager at fastmail.ca Mon Jun 27 02:08:17 2005 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Mon, 27 Jun 2005 06:08:17 +0000 (UTC) Subject: [BiO BB] difference between Refseq and Uniprot In-Reply-To: <42BE64E6.7020903@gmail.com> Message-ID: <20050627060820.A1017861CD9@mail.interchange.ca> It's redundancy both in Uniprot and In Refseq. Refseq contain splice variants but no fragments, it has good coverage. While SwissProt doesn't contain fragments or spice variants, but the coverage isn't quite as good. But TrEMBL does contain fragments and splice variants. For a few species the IPI database could be an alternative http://www.ebi.ac.uk/IPI/IPIhelp.html . It's a mergeer of UniProt, RefSeq and Ensembl. IPI has good coverage, and it contains splice variants, but few fragments. Stefanie > Hi, all, > > Recently, I am working on the protein sequence analysis. I found the > Refseq is very different from Uniprot. Uniprot contains much more > proteins if TrEMBL is included. Can any experts give some comments on > these two protein database. Which one is more reliable? It seems > Swiss is of the best quality, then Refseq, then TrEMBL. And also, It > seems there are redundancy in Uniprot. Is that so? > > -Frank > > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From dmb at mrc-dunn.cam.ac.uk Mon Jun 27 04:11:49 2005 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Mon, 27 Jun 2005 09:11:49 +0100 (BST) Subject: [BiO BB] difference between Refseq and Uniprot In-Reply-To: <20050627060820.A1017861CD9@mail.interchange.ca> References: <42BE64E6.7020903@gmail.com> <20050627060820.A1017861CD9@mail.interchange.ca> Message-ID: <39970.141.14.23.109.1119859909.squirrel@www.mrc-dunn.cam.ac.uk> When it comes to redundancy its good to be specific about what you mean, biological redundancy or sequence redundancy? I know refseq tries to specifically remove biological redundancy (collecting together duplicate copies of the same genes). The sequence redundancy is removed in uniprot in the uniparc sequence database. Also SwissProt keeps spice variant information implicit in comment lines which you can parse to get the variant sequences (this is what they do in uniparc). How does Refseq deal with splice variants / sequence redundancy? Has anyone done large scale comparison of the two databases? Cheers, Dan. ++ Stefanie Lager-- > It's redundancy both in Uniprot and In Refseq. Refseq contain splice > variants but no fragments, it has good coverage. While SwissProt doesn't > contain fragments or spice variants, but the coverage isn't quite as > good. But TrEMBL does contain fragments and splice variants. For a few > species the IPI database could be an alternative > http://www.ebi.ac.uk/IPI/IPIhelp.html . It's a mergeer of UniProt, > RefSeq and Ensembl. IPI has good coverage, and it contains splice > variants, but few fragments. > > Stefanie > >> Hi, all, >> >> Recently, I am working on the protein sequence analysis. I found the >> Refseq is very different from Uniprot. Uniprot contains much more >> proteins if TrEMBL is included. Can any experts give some comments on >> these two protein database. Which one is more reliable? It seems >> Swiss is of the best quality, then Refseq, then TrEMBL. And also, It >> seems there are redundancy in Uniprot. Is that so? >> >> -Frank >> >> >> _______________________________________________ >> Bioinformatics.Org general forum - >> BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > _________________________________________________________________ > http://fastmail.ca/ - Fast Secure Web Email for Canadians > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From lifei03 at gmail.com Mon Jun 27 07:09:08 2005 From: lifei03 at gmail.com (Frank Lee) Date: Mon, 27 Jun 2005 19:09:08 +0800 Subject: [BiO BB] difference between Refseq and Uniprot In-Reply-To: <39970.141.14.23.109.1119859909.squirrel@www.mrc-dunn.cam.ac.uk> References: <42BE64E6.7020903@gmail.com> <20050627060820.A1017861CD9@mail.interchange.ca> <39970.141.14.23.109.1119859909.squirrel@www.mrc-dunn.cam.ac.uk> Message-ID: <42BFDE54.3050104@gmail.com> From the gpff.gz file in Refseq database, transcrpit varaiants of genes are given as independant items. I am giving an example of transcrpits annotation in RefSeq database here LOCUS NP_739577 433 aa linear PRI 27-OCT-2004 ................... Transcript Variant: This variant (2) lacks an in-frame segment of the coding region, compared to variant 1. It encodes a shorter isoform (2), that is missing an internal segment compared to isoform 1. ................ -Frank Dan Bolser wrote: >When it comes to redundancy its good to be specific about what you mean, biological >redundancy or sequence redundancy? I know refseq tries to specifically remove >biological redundancy (collecting together duplicate copies of the same genes). The >sequence redundancy is removed in uniprot in the uniparc sequence database. > >Also SwissProt keeps spice variant information implicit in comment lines which you >can parse to get the variant sequences (this is what they do in uniparc). > >How does Refseq deal with splice variants / sequence redundancy? > >Has anyone done large scale comparison of the two databases? > >Cheers, >Dan. > > >++ Stefanie Lager-- > > >>It's redundancy both in Uniprot and In Refseq. Refseq contain splice >>variants but no fragments, it has good coverage. While SwissProt doesn't >>contain fragments or spice variants, but the coverage isn't quite as >>good. But TrEMBL does contain fragments and splice variants. For a few >>species the IPI database could be an alternative >>http://www.ebi.ac.uk/IPI/IPIhelp.html . It's a mergeer of UniProt, >>RefSeq and Ensembl. IPI has good coverage, and it contains splice >>variants, but few fragments. >> >>Stefanie >> >> >> >>>Hi, all, >>> >>>Recently, I am working on the protein sequence analysis. I found the >>>Refseq is very different from Uniprot. Uniprot contains much more >>>proteins if TrEMBL is included. Can any experts give some comments on >>>these two protein database. Which one is more reliable? It seems >>>Swiss is of the best quality, then Refseq, then TrEMBL. And also, It >>>seems there are redundancy in Uniprot. Is that so? >>> >>>-Frank >>> >>> >>>_______________________________________________ >>>Bioinformatics.Org general forum - >>>BiO_Bulletin_Board at bioinformatics.org >>>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >>> >>> >>_________________________________________________________________ >> http://fastmail.ca/ - Fast Secure Web Email for Canadians >> >>_______________________________________________ >>Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> >> > > >_______________________________________________ >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > From lifei03 at gmail.com Tue Jun 28 03:40:20 2005 From: lifei03 at gmail.com (Frank Lee) Date: Tue, 28 Jun 2005 15:40:20 +0800 Subject: [BiO BB] difference between Refseq and Uniprot In-Reply-To: <39970.141.14.23.109.1119859909.squirrel@www.mrc-dunn.cam.ac.uk> References: <42BE64E6.7020903@gmail.com> <20050627060820.A1017861CD9@mail.interchange.ca> <39970.141.14.23.109.1119859909.squirrel@www.mrc-dunn.cam.ac.uk> Message-ID: <42C0FEE4.8070103@gmail.com> Hi, all, I need transfer my Refseq ID to uniprot ID. does anyone have this experience. Thanks. Frank Dan Bolser wrote: >When it comes to redundancy its good to be specific about what you mean, biological >redundancy or sequence redundancy? I know refseq tries to specifically remove >biological redundancy (collecting together duplicate copies of the same genes). The >sequence redundancy is removed in uniprot in the uniparc sequence database. > >Also SwissProt keeps spice variant information implicit in comment lines which you >can parse to get the variant sequences (this is what they do in uniparc). > >How does Refseq deal with splice variants / sequence redundancy? > >Has anyone done large scale comparison of the two databases? > >Cheers, >Dan. > > >++ Stefanie Lager-- > > >>It's redundancy both in Uniprot and In Refseq. Refseq contain splice >>variants but no fragments, it has good coverage. While SwissProt doesn't >>contain fragments or spice variants, but the coverage isn't quite as >>good. But TrEMBL does contain fragments and splice variants. For a few >>species the IPI database could be an alternative >>http://www.ebi.ac.uk/IPI/IPIhelp.html . It's a mergeer of UniProt, >>RefSeq and Ensembl. IPI has good coverage, and it contains splice >>variants, but few fragments. >> >>Stefanie >> >> >> >>>Hi, all, >>> >>>Recently, I am working on the protein sequence analysis. I found the >>>Refseq is very different from Uniprot. Uniprot contains much more >>>proteins if TrEMBL is included. Can any experts give some comments on >>>these two protein database. Which one is more reliable? It seems >>>Swiss is of the best quality, then Refseq, then TrEMBL. And also, It >>>seems there are redundancy in Uniprot. Is that so? >>> >>>-Frank >>> >>> >>>_______________________________________________ >>>Bioinformatics.Org general forum - >>>BiO_Bulletin_Board at bioinformatics.org >>>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >>> >>> >>_________________________________________________________________ >> http://fastmail.ca/ - Fast Secure Web Email for Canadians >> >>_______________________________________________ >>Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> >> > > >_______________________________________________ >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > From lray at albany.edu Wed Jun 29 11:46:07 2005 From: lray at albany.edu (Lipika Ray) Date: Wed, 29 Jun 2005 11:46:07 -0400 (EDT) Subject: [BiO BB] Protein domain Message-ID: <1483.169.226.137.250.1120059967.squirrel@169.226.137.250> Hi, I just want to know that how will you distinguish between a structural and functional domain of a protein? In other words, what is structural domain and functional domain? I think from SCOP, CATH type of databases, we can get the information about structural domains. If I am right, then where from can we get the information about functional domain of a protein? Thanking you, Lipika Ray +++++++++++++++++++++++++++++++++++++++++ Dr. Lipika Ray Postdoctoral researcher SUNY, UAlbany From adarshramakumar at yahoo.co.uk Wed Jun 29 16:37:09 2005 From: adarshramakumar at yahoo.co.uk (Adarsh Ramakumar) Date: Wed, 29 Jun 2005 21:37:09 +0100 (BST) Subject: [BiO BB] Protein domain In-Reply-To: <1483.169.226.137.250.1120059967.squirrel@169.226.137.250> Message-ID: <20050629203709.72270.qmail@web25501.mail.ukl.yahoo.com> Pfam, SMART databases are suggestive of functional domains. --- Lipika Ray wrote: > Hi, > > I just want to know that how will you distinguish > between a structural and > functional domain of a protein? In other words, what > is structural domain > and functional domain? I think from SCOP, CATH type > of databases, we can > get the information about structural domains. If I > am right, then where > from can we get the information about functional > domain of a protein? > > Thanking you, > > Lipika Ray > > +++++++++++++++++++++++++++++++++++++++++ > Dr. Lipika Ray > Postdoctoral researcher > SUNY, UAlbany > > > > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ___________________________________________________________ How much free photo storage do you get? Store your holiday snaps for FREE with Yahoo! Photos http://uk.photos.yahoo.com From o.medina at gmx.net Wed Jun 29 18:20:05 2005 From: o.medina at gmx.net (Oscar Medina) Date: Wed, 29 Jun 2005 17:20:05 -0500 Subject: [BiO BB] PDB In-Reply-To: <20050629203709.72270.qmail@web25501.mail.ukl.yahoo.com> References: <20050629203709.72270.qmail@web25501.mail.ukl.yahoo.com> Message-ID: <42C31E95.3090106@gmx.net> Hi: I wonder if I can download all the PDB database for local analysis. If so, where is it available? Thank you Oscar Medina From operon at cbiot.ufrgs.br Wed Jun 29 18:36:01 2005 From: operon at cbiot.ufrgs.br (Marcos Oliveira de Carvalho) Date: Wed, 29 Jun 2005 19:36:01 -0300 Subject: [BiO BB] PDB In-Reply-To: <42C31E95.3090106@gmx.net> References: <20050629203709.72270.qmail@web25501.mail.ukl.yahoo.com> <42C31E95.3090106@gmx.net> Message-ID: ftp://ftp.rcsb.org/pub/pdb/ On Wed, 29 Jun 2005 19:20:05 -0300, Oscar Medina wrote: > Hi: > > I wonder if I can download all the PDB database for local analysis. If > so, where is it available? > > Thank you > > Oscar Medina > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From virajj at lycos.com Wed Jun 29 21:47:43 2005 From: virajj at lycos.com (vijaya raj) Date: Wed, 29 Jun 2005 20:47:43 -0500 Subject: [BiO BB] PDB Message-ID: <20050630014743.15D5CE5BC7@ws7-2.us4.outblaze.com> hi there was an option to write to PDB and get copies of the latest database as CD-ROM distribution... chek it out from PDB website... http://www.rcsb.org/pdb/data_cd.html ------------ vijayaraj nagarajan department of biological sciences the university of southern mississippi ms, usa -- _______________________________________________ NEW! Lycos Dating Search. The only place to search multiple dating sites at once. http://datingsearch.lycos.com From nanomuthu at yahoo.co.in Thu Jun 30 03:22:29 2005 From: nanomuthu at yahoo.co.in (Muthukumar singaravelu) Date: Thu, 30 Jun 2005 08:22:29 +0100 (BST) Subject: [BiO BB] PDB In-Reply-To: <20050630014743.15D5CE5BC7@ws7-2.us4.outblaze.com> Message-ID: <20050630072229.83532.qmail@web8510.mail.in.yahoo.com> Hai I got those CD's but how to get the pdb files from it. Can you help me since it has got only txt files and others but not the pdb files. how to extract the pdb from those. I am in need of it for a small project pls help me to proceed further. Thank you, vijaya raj wrote: hi there was an option to write to PDB and get copies of the latest database as CD-ROM distribution... chek it out from PDB website... http://www.rcsb.org/pdb/data_cd.html ------------ vijayaraj nagarajan department of biological sciences the university of southern mississippi ms, usa -- _______________________________________________ NEW! Lycos Dating Search. The only place to search multiple dating sites at once. http://datingsearch.lycos.com _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board S.Muthukumar Junior Research Fellow Bioinfromatics National Institute of Ocean Technology, Chennai - 601 302, TN, India. Mobile: +91-9840281476 Docking Marine Biology @ http://www.niot.res.in:82/mbic/default.asp --------------------------------- How much free photo storage do you get? Store your friends n family photos for FREE with Yahoo! Photos. http://in.photos.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From virajj at lycos.com Thu Jun 30 09:54:39 2005 From: virajj at lycos.com (vijaya raj) Date: Thu, 30 Jun 2005 08:54:39 -0500 Subject: [BiO BB] PDB Message-ID: <20050630135439.42105C6119@ws7-5.us4.outblaze.com> hey you must have got CDs with two types of contents, one with the actual data (PDB files) and the other with experimental details... chek it out. sometimes if you had requested only for the experimental details you might not have got the actual data CD. in that case just download it from the pdb ftp site, if you need it urgently...or write to pdb to get the data CD. goodluk vijay ----- Original Message ----- From: "Muthukumar singaravelu" To: "The general forum at Bioinformatics.Org" Subject: Re: [BiO BB] PDB Date: Thu, 30 Jun 2005 08:22:29 +0100 (BST) > > Hai > > I got those CD's but how to get the pdb files from it. Can you > help me since it has got only txt files and others but not the pdb > files. how to extract the pdb from those. I am in need of it for a > small project pls help me to proceed further. > > Thank you, > > vijaya raj wrote: > hi > there was an option to write to PDB and get copies of the latest > database as CD-ROM distribution... chek it out from PDB website... > http://www.rcsb.org/pdb/data_cd.html > > ------------ > vijayaraj nagarajan > department of biological sciences > the university of southern mississippi > ms, usa > > > > -- > _______________________________________________ > NEW! Lycos Dating Search. The only place to search multiple dating > sites at once. > http://datingsearch.lycos.com > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > S.Muthukumar > Junior Research Fellow Bioinfromatics > National Institute of Ocean Technology, > Chennai - 601 302, TN, India. > Mobile: +91-9840281476 > Docking Marine Biology @ http://www.niot.res.in:82/mbic/default.asp > > > > > > --------------------------------- > How much free photo storage do you get? Store your friends n family > photos for FREE with Yahoo! Photos. > http://in.photos.yahoo.com > > > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board ------------ vijayaraj nagarajan department of biological sciences the university of southern mississippi ms, usa -- _______________________________________________ NEW! Lycos Dating Search. The only place to search multiple dating sites at once. http://datingsearch.lycos.com From ritinsharma at rediffmail.com Mon Jun 27 02:33:17 2005 From: ritinsharma at rediffmail.com (ritin sharma) Date: 27 Jun 2005 06:33:17 -0000 Subject: [BiO BB] help required on insight Message-ID: <20050627063317.15575.qmail@webmail29.rediffmail.com> ? Hello bioinformaticians, I have modelled a protein(receptor) using modeller. Now i want to do some minimization on my receptor and ligand and later docking using insight. But i have got stuck with fixing potentials and charges of both my receptor and ligand. I get various errors like "Partial charges not equal to formal charges" , "open or undefined valencies", "cannot assign cvff forcefeild". While running discover it complains of unfound parameters in .out file and run is stopped. My ligand is a nonapeptide and has a -S03H group attached to tyrosine aswell as -NH2 attached to phenylalanine. I am using CVFF forcefield. My receptor is purely made of amino acids. Anyone who has faced similar difficulty, please let me know the solution. If anyone has good tutorials on performing minimization, interactive and automated docking using insight than please send me the link or material. Any help in this regard will be highly appreciated. Respond ASAP Yours sincerely Ritin Sharma -------------- next part -------------- An HTML attachment was scrubbed... URL: