From info at nanoaging.com Fri Jul 1 19:28:59 2005 From: info at nanoaging.com (The NanoAging Institute) Date: Fri, 1 Jul 2005 18:28:59 -0500 Subject: [BiO BB] Data Mining Message-ID: <000601c57e94$a8b4fbe0$cb337a18@nomxx5ybrzvkgn> Does anybody know what kind of software would be useful to work for the aging/senescence process? --Jon -------------- next part -------------- An HTML attachment was scrubbed... URL: From utabiodb at gmail.com Sat Jul 2 12:35:06 2005 From: utabiodb at gmail.com (Zoe Raja) Date: Sat, 2 Jul 2005 12:35:06 -0400 Subject: [BiO BB] Survey researching usability of Bio Databases Message-ID: Hello all, I am researching usability of Bio Databases for my Master's Thesis and would like researchers to contribute their insights via my survey and/or telephone interviews. If you have used Biological Databases such as SWISS-PROT, PDB, GENBANK, EMBL or others, please contribute your insights and opinions about how those databases were able to help you in your research, and more importantly what limitations or frustration did you encounter when using them? A downloadable survey is available here: -------------------------------------------------------- http://students.uta.edu/za/zar5695 -------------------------------------------------------- It will only take a few moments to complete, when you are done email it to me at: UTABioDB at gmail.com I am also planning to include interviews in my study, if you or someone you know would like to discuss your experience with and how Biological Databases could be improved I can telephone you or, if you prefer send a detailed written reply. Researchers both in and outside the USA are welcome. For your privacy, your name and institution will not be included in the thesis unless you specifically request it. Thanks, Zoe UTABioDB at gmail.com From M.Liebman at wriwindber.org Sat Jul 2 13:07:17 2005 From: M.Liebman at wriwindber.org (Michael Liebman) Date: Sat, 2 Jul 2005 13:07:17 -0400 Subject: [BiO BB] Data Mining Message-ID: <7690673B79E70D429A1205791933922309FAC7@wri-xchng.WRIWINDBER.ORG> What are you looking for, exactly- we do both extensive data mining and text data mining and have been developing an Ontology to represent development and aging processes. Michael Michael N. Liebman, PhD Chief Scientific Officer Windber Research Institute 600 Somerset Ave Windber, PA 15963 (814) 467 9844 office (814) 467 6334 fax (814) 659 5450 cell ________________________________ From: bio_bulletin_board-bounces+m.liebman=wriwindber.org at bioinformatics.org [mailto:bio_bulletin_board-bounces+m.liebman=wriwindber.org at bioinformati cs.org] On Behalf Of The NanoAging Institute Sent: Friday, July 01, 2005 7:29 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Data Mining Does anybody know what kind of software would be useful to work for the aging/senescence process? --Jon -------------- next part -------------- An HTML attachment was scrubbed... URL: From smagarwal at yahoo.com Wed Jul 6 10:40:33 2005 From: smagarwal at yahoo.com (Subhash Agarwal) Date: Wed, 6 Jul 2005 15:40:33 +0100 (BST) Subject: [BiO BB] Mol2 to PDB Message-ID: <20050706144033.72298.qmail@web31501.mail.mud.yahoo.com> Hi all I need to convert some chemical molecules which are in .mol2 format to PDB format. When i try to do so using Insight what i find is that bond information is lost. Can anybody suggest me a way for converting .mol2 format to PDB format so that the bond information is not lost. Thanks Subhash __________________________________________________________ Free antispam, antivirus and 1GB to save all your messages Only in Yahoo! Mail: http://in.mail.yahoo.com From jwester at sgi1.chemie.uni-hamburg.de Wed Jul 6 10:59:58 2005 From: jwester at sgi1.chemie.uni-hamburg.de (Jan-Christoph Westermann) Date: Wed, 06 Jul 2005 16:59:58 +0200 Subject: [BiO BB] Mol2 to PDB In-Reply-To: <20050706144033.72298.qmail@web31501.mail.mud.yahoo.com> References: <20050706144033.72298.qmail@web31501.mail.mud.yahoo.com> Message-ID: <42CBF1EE.4060401@sgi1.chemie.uni-hamburg.de> Subhash Agarwal schrieb: > Hi all > > I need to convert some chemical molecules which are in > .mol2 format to PDB format. When i try to do so using > Insight what i find is that bond information is lost. > > Can anybody suggest me a way for converting .mol2 > format to PDB format so that the bond information is > not lost. Try Open Babel. http://openbabel.sourceforge.net/ HTH, jcw From letondal at pasteur.fr Wed Jul 6 14:52:33 2005 From: letondal at pasteur.fr (Catherine Letondal) Date: Wed, 6 Jul 2005 20:52:33 +0200 Subject: [BiO BB] Course in Informatics for Biology 2006 at Institut Pasteur Message-ID: <90353a1d3ce952b31ff4cd833501a115@pasteur.fr> Hi, ************************************************************************ * Course in informatics for biology 2006 at Institut Pasteur http://www.pasteur.fr/formation/infobio-en.html ************************************************************************ * In the series of courses offered at the Pasteur Institute, a course will be offered in informatics in biology. The next session will take place from January to end of April 2006. The main goal of this course is to provide researchers in biology an initial exposure to informatics. Admitance in the course is reserved for those with a degree in biology or a related discipline. With more and more bioinformatics tools available, it becomes increasingly important for researchers in biology to be able both to manage their data, implement their ideas, and judge for themselves the usefulness of new algorithms and software. This course will emphasize fundamental aspects of computer science and apply them to biological examples. Theoretical aspects (algorithm development, logic, problem modeling and design methods), and technical applications (databases and web technologies) that are relevant for biologists will be thoroughly discussed. Programming is presented through the object-oriented paradigm, using a modern high-level language, Python, provided with tools for biology and enabling both prototyping or scripting and the building of important software systems. Learning of additional languages (perl and C) will be available for interested students. Learning during the course will be reinforced with computing exercises, and effective training will be provided by a 2 month research project. The working language of the course is French. For further information, please consult: http://www.pasteur.fr/formation/infobio-en.html *** Registration will be closed on October 15 2005. *** Sincerely, -- Catherine Letondal, Institut Pasteur & Katja Schuerer, Genomining Course informatics for biology -- www.pasteur.fr/formation/infobio From forward at hongyu.org Wed Jul 6 17:03:35 2005 From: forward at hongyu.org (forward at hongyu.org) Date: Wed, 6 Jul 2005 14:03:35 -0700 (PDT) Subject: [BiO BB] electrostatic map of proteins Message-ID: <50781.71.109.241.43.1120683815.squirrel@hongyu.org> Dear all, I need to find a program on Windows or Linux to generate electrostatic maps of proteins with known 3D structures. Since it's a just a pilot project of mine, I am not interested in purchasing big commercial packages like Insight II. GRASP is cool, but it only ran on SGI the last time when I used it, which is a long time ago. I would very appreciate your advice. From operon at cbiot.ufrgs.br Wed Jul 6 17:23:07 2005 From: operon at cbiot.ufrgs.br (Marcos Oliveira de Carvalho) Date: Wed, 06 Jul 2005 18:23:07 -0300 Subject: [BiO BB] electrostatic map of proteins In-Reply-To: <50781.71.109.241.43.1120683815.squirrel@hongyu.org> References: <50781.71.109.241.43.1120683815.squirrel@hongyu.org> Message-ID: try pymol or chimera. http://www.cgl.ucsf.edu/chimera/ http://pymol.sourceforge.net/ m. On Wed, 06 Jul 2005 18:03:35 -0300, wrote: > > Dear all, > > I need to find a program on Windows or Linux to generate electrostatic > maps of proteins with known 3D structures. Since it's a just a pilot > project of mine, I am not interested in purchasing big commercial > packages > like Insight II. GRASP is cool, but it only ran on SGI the last time when > I used it, which is a long time ago. > > I would very appreciate your advice. > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From forward at hongyu.org Wed Jul 6 18:22:28 2005 From: forward at hongyu.org (forward at hongyu.org) Date: Wed, 6 Jul 2005 15:22:28 -0700 (PDT) Subject: [BiO BB] electrostatic map of proteins In-Reply-To: References: <50781.71.109.241.43.1120683815.squirrel@hongyu.org> Message-ID: <50602.71.109.241.43.1120688548.squirrel@hongyu.org> Thanks, Marcos, but those are just plain graphic softwares. I need something like GRASP, which can not only show 3D graphics, but also is able to calculate and display electro-static poential distributions on the protein surface. On Wed, July 6, 2005 2:23 pm, Marcos Oliveira de Carvalho said: > > > try pymol or chimera. > > http://www.cgl.ucsf.edu/chimera/ > http://pymol.sourceforge.net/ > > m. > > > On Wed, 06 Jul 2005 18:03:35 -0300, wrote: > >> >> Dear all, >> >> I need to find a program on Windows or Linux to generate electrostatic >> maps of proteins with known 3D structures. Since it's a just a pilot >> project of mine, I am not interested in purchasing big commercial >> packages >> like Insight II. GRASP is cool, but it only ran on SGI the last time >> when >> I used it, which is a long time ago. >> >> I would very appreciate your advice. >> _______________________________________________ >> Bioinformatics.Org general forum - >> BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > -- From virajj at lycos.com Wed Jul 6 18:38:42 2005 From: virajj at lycos.com (vijaya raj) Date: Wed, 06 Jul 2005 17:38:42 -0500 Subject: [BiO BB] electrostatic map of proteins Message-ID: <20050706223842.910CF86B10@ws7-1.us4.outblaze.com> cant SPDBV do that... ----- Original Message ----- From: forward at hongyu.org To: "Marcos Oliveira de Carvalho" Subject: Re: [BiO BB] electrostatic map of proteins Date: Wed, 6 Jul 2005 15:22:28 -0700 (PDT) > > Thanks, Marcos, but those are just plain graphic softwares. > > I need something like GRASP, which can not only show 3D graphics, but also > is able to calculate and display electro-static poential distributions on > the protein surface. > > On Wed, July 6, 2005 2:23 pm, Marcos Oliveira de Carvalho said: > > > > > > try pymol or chimera. > > > > http://www.cgl.ucsf.edu/chimera/ > > http://pymol.sourceforge.net/ > > > > m. > > > > > > On Wed, 06 Jul 2005 18:03:35 -0300, wrote: > > > >> > >> Dear all, > >> > >> I need to find a program on Windows or Linux to generate electrostatic > >> maps of proteins with known 3D structures. Since it's a just a pilot > >> project of mine, I am not interested in purchasing big commercial > >> packages > >> like Insight II. GRASP is cool, but it only ran on SGI the last time > >> when > >> I used it, which is a long time ago. > >> > >> I would very appreciate your advice. > >> _______________________________________________ > >> 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 ------------ 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 jstroud at mbi.ucla.edu Wed Jul 6 18:49:04 2005 From: jstroud at mbi.ucla.edu (James Stroud) Date: Wed, 6 Jul 2005 15:49:04 -0700 Subject: [BiO BB] electrostatic map of proteins In-Reply-To: <50602.71.109.241.43.1120688548.squirrel@hongyu.org> References: <50781.71.109.241.43.1120683815.squirrel@hongyu.org> <50602.71.109.241.43.1120688548.squirrel@hongyu.org> Message-ID: <200507061549.04615.jstroud@mbi.ucla.edu> Submit your question to the CCP4 bulletin board. You will get very good answers there. Also, you may want to plunk down the $500 for delphi from the Honig lab. I understand this is the best PB solver around. If you get it, check this page out: http://keres.colorado.edu/howto/delphi-surface-pymol.html Also, I think spdb viewer has a built in pb calculator, but I'm not sure how good it is. James On Wednesday 06 July 2005 03:22 pm, forward at hongyu.org wrote: > Thanks, Marcos, but those are just plain graphic softwares. > > I need something like GRASP, which can not only show 3D graphics, but also > is able to calculate and display electro-static poential distributions on > the protein surface. > > On Wed, July 6, 2005 2:23 pm, Marcos Oliveira de Carvalho said: > > try pymol or chimera. > > > > http://www.cgl.ucsf.edu/chimera/ > > http://pymol.sourceforge.net/ > > > > m. > > > > On Wed, 06 Jul 2005 18:03:35 -0300, wrote: > >> Dear all, > >> > >> I need to find a program on Windows or Linux to generate electrostatic > >> maps of proteins with known 3D structures. Since it's a just a pilot > >> project of mine, I am not interested in purchasing big commercial > >> packages > >> like Insight II. GRASP is cool, but it only ran on SGI the last time > >> when > >> I used it, which is a long time ago. > >> > >> I would very appreciate your advice. > >> _______________________________________________ > >> Bioinformatics.Org general forum - > >> BiO_Bulletin_Board at bioinformatics.org > >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com/ From elavv2003 at gmail.com Thu Jul 7 00:02:20 2005 From: elavv2003 at gmail.com (Elavazhagan) Date: Thu, 7 Jul 2005 09:32:20 +0530 Subject: [BiO BB] how to interpret docking result Message-ID: Hai, Kindly any one suggest me how to interpret ther docking result. Thanks. -- E.Elavazhagan 09444332083 -------------- next part -------------- An HTML attachment was scrubbed... URL: From dmb at mrc-dunn.cam.ac.uk Thu Jul 7 04:19:56 2005 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 7 Jul 2005 09:19:56 +0100 (BST) Subject: [BiO BB] electrostatic map of proteins In-Reply-To: <200507061549.04615.jstroud@mbi.ucla.edu> Message-ID: On Wed, 6 Jul 2005, James Stroud wrote: >Submit your question to the CCP4 bulletin board. You will get very good >answers there. > >Also, you may want to plunk down the $500 for delphi from the Honig lab. I >understand this is the best PB solver around. If you get it, check this page >out: > >http://keres.colorado.edu/howto/delphi-surface-pymol.html Any screen shots :) > >Also, I think spdb viewer has a built in pb calculator, but I'm not sure how >good it is. > >James > >On Wednesday 06 July 2005 03:22 pm, forward at hongyu.org wrote: >> Thanks, Marcos, but those are just plain graphic softwares. >> >> I need something like GRASP, which can not only show 3D graphics, but also >> is able to calculate and display electro-static poential distributions on >> the protein surface. >> >> On Wed, July 6, 2005 2:23 pm, Marcos Oliveira de Carvalho said: >> > try pymol or chimera. >> > >> > http://www.cgl.ucsf.edu/chimera/ >> > http://pymol.sourceforge.net/ >> > >> > m. >> > >> > On Wed, 06 Jul 2005 18:03:35 -0300, wrote: >> >> Dear all, >> >> >> >> I need to find a program on Windows or Linux to generate electrostatic >> >> maps of proteins with known 3D structures. Since it's a just a pilot >> >> project of mine, I am not interested in purchasing big commercial >> >> packages >> >> like Insight II. GRASP is cool, but it only ran on SGI the last time >> >> when >> >> I used it, which is a long time ago. >> >> >> >> I would very appreciate your advice. >> >> _______________________________________________ >> >> Bioinformatics.Org general forum - >> >> BiO_Bulletin_Board at bioinformatics.org >> >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From virajj at lycos.com Thu Jul 7 09:58:23 2005 From: virajj at lycos.com (vijaya raj) Date: Thu, 07 Jul 2005 08:58:23 -0500 Subject: [BiO BB] how to interpret docking result Message-ID: <20050707135824.09090E5BC7@ws7-2.us4.outblaze.com> An embedded and charset-unspecified text was scrubbed... Name: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From x.sole at ico.scs.es Thu Jul 7 10:20:17 2005 From: x.sole at ico.scs.es (Sole Acha, Xavi) Date: Thu, 7 Jul 2005 16:20:17 +0200 Subject: [BiO BB] Unigene database in relational format Message-ID: <5FF3F11444E3A9439191AA1EDCB69A1721CEFC@icosrvmail01.ICO.SCS.local> Hello all, I would like to know if it is possible to find/download the Unigene Database in a relational database format. I want to store Unigene info in a local database, but before attempting to program a parser for the text file you can download from NCBI's website I wanted to be sure that there is no way of finding the database in ascii "table-like" text files, so they can easily be dumped onto a database. Thank you very much in advance. Xavier. From dmb at mrc-dunn.cam.ac.uk Thu Jul 7 10:41:15 2005 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 7 Jul 2005 15:41:15 +0100 (BST) Subject: [BiO BB] Unigene database in relational format In-Reply-To: <5FF3F11444E3A9439191AA1EDCB69A1721CEFC@icosrvmail01.ICO.SCS.local> Message-ID: On Thu, 7 Jul 2005, Sole Acha, Xavi wrote: >Hello all, > >I would like to know if it is possible to find/download the Unigene >Database in a relational database format. I want to store Unigene info >in a local database, but before attempting to program a parser for the >text file you can download from NCBI's website I wanted to be sure that >there is no way of finding the database in ascii "table-like" text >files, so they can easily be dumped onto a database. > >Thank you very much in advance. Did you try BioSQL? > >Xavier. >_______________________________________________ >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From dmnunif at charter.net Thu Jul 7 16:28:33 2005 From: dmnunif at charter.net (D. Norris) Date: Thu, 7 Jul 2005 15:28:33 -0500 Subject: [BiO BB] Thiol/Disulfide Environmental Energy Exchange Code Message-ID: <002a01c58332$72739cb0$3382c418@VALUED4DA88152> To Those Interested In Mechanistically How A Messenger Chemical Group or Energy State Is Encoded Into Information In Biological Systems (i.e., Viruses, Whole Cells, and Multicellular Organisms): After over 40 years of systems-biology research on the unifying dynamic qualitative and quantitative mechanistic means of the transduction of messenger chemical groups and energy states into information in biological systems, the scientists at Unifinium Ltd have solidly confirmed repeatedly in peer-reviewed published papers that the unifying mechanism is Thiol (-SH) / Disulfide (-S-S-) Exchange Protein Biophysics. The necessary unifying messenger (UM) is sulfur exchange (electro) chemistry; and -SH, its derivatives, and its redox couple, i.e., -S-S-, are the specific means by which the UM is used to create the qualitative and quantitative bioinformation. Our pertinent original research findings were first published in "Nature" in 1969; "Science" 1970; "Experientia" 1971; etc., "Nature" in 1973, & 1975; etc.; "Bioelectrochem. Bioenerget.", in 1985; "J Chem Ecol", in 1988; a chapter in the book "Functional Dynamics of Phytophagous Insects", edited by Ananthakrishnan, published by Oxford & IBH Publishing, New Delhi, 1994; and reviewed extensively in a chapter in the book, "Predators and Parasitoids" , edited by Koul and Dhaliwal, published by Taylor & Francis, London, in 2003. A review recently was rejected by "Antioxidant & Redox Signaling" especially because it was "Too Broad". Our research has been broad in scope, and it is very broadly pertinent and valid. Have a read; it will not be a waste of time for those who are really interested in energy transduction into bioinformation in whole biological systems. dmn. P.S. If our research does not deal with bioinformatics, then we do not mind the "misfit". -------------- next part -------------- An HTML attachment was scrubbed... URL: From vetdebarshi at gmail.com Fri Jul 8 11:56:00 2005 From: vetdebarshi at gmail.com (debarshi roy) Date: Fri, 8 Jul 2005 08:56:00 -0700 Subject: [BiO BB] Thiol/Disulfide Environmental Energy Exchange Code In-Reply-To: <002a01c58332$72739cb0$3382c418@VALUED4DA88152> References: <002a01c58332$72739cb0$3382c418@VALUED4DA88152> Message-ID: <959075805070808566c9771e7@mail.gmail.com> Hello, I would like to know if there is any online free course`available in Bioinformatics for the iernational students in USA? The course offered by Bitmap is purely for US citizens. Please inform me. Thanks Debarshi Roy On 7/7/05, D. Norris wrote: > > To Those Interested In Mechanistically How A Messenger Chemical Group or > Energy State Is Encoded Into Information In Biological Systems (i.e., > Viruses, Whole Cells, and Multicellular Organisms): > > After over 40 years of systems-biology research on the unifying dynamic > qualitative and quantitative mechanistic means of the transduction of > messenger chemical groups and energy states into information in biological > systems, the scientists at Unifinium Ltd have solidly confirmed repeatedly > in peer-reviewed published papers that the unifying mechanism is Thiol (-SH) > / Disulfide (-S-S-) Exchange Protein Biophysics. The necessary unifying > messenger (UM) is sulfur exchange (electro) chemistry; and -SH, its > derivatives, and its redox couple, i.e., -S-S-, are the specific means by > which the UM is used to create the qualitative and quantitative > bioinformation. Our pertinent original research findings were first > published in "Nature" in 1969; "Science" 1970; "Experientia" 1971; etc., > "Nature" in 1973, & 1975; etc.; "Bioelectrochem. Bioenerget.", in 1985; "J > Chem Ecol", in 1988; a chapter in the book "Functional Dynamics of > Phytophagous Insects", edited by Ananthakrishnan, published by Oxford & IBH > Publishing, New Delhi, 1994; and reviewed extensively in a chapter in the > book, "Predators and Parasitoids" , edited by Koul and Dhaliwal, published > by Taylor & Francis, London, in 2003. > A review recently was rejected by "Antioxidant & Redox Signaling" especially > because it was "Too Broad". Our research has been broad in scope, and it is > very broadly pertinent and valid. Have a read; it will not be a waste of > time for those who are really interested in energy transduction into > bioinformation in whole biological systems. dmn. > > P.S. If our research does not deal with bioinformatics, then we do not mind > the "misfit". > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > From elavv2003 at gmail.com Thu Jul 7 00:00:31 2005 From: elavv2003 at gmail.com (Elavazhagan) Date: Thu, 7 Jul 2005 09:30:31 +0530 Subject: [BiO BB] Re: BiO_Bulletin_Board Digest, Vol 9, Issue 3 In-Reply-To: <20050706160044.0C916D1F1A@www.bioinformatics.org> References: <20050706160044.0C916D1F1A@www.bioinformatics.org> Message-ID: Hai, I suggest u to choose Dundee prodrug server to perform file conversion where u can draw the molecule using JME editor,it will be converted to huge number of formats.U can choose what ever u want.U can also optimise the molecule .u can get it through http://davapc1.bioch.dundee.ac.uk/programs/prodrg/. I hope it helps. Bye. On 7/6/05, bio_bulletin_board-request at bioinformatics.org < 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. Mol2 to PDB (Subhash Agarwal) > 2. Re: Mol2 to PDB (Jan-Christoph Westermann) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 6 Jul 2005 15:40:33 +0100 (BST) > From: Subhash Agarwal > Subject: [BiO BB] Mol2 to PDB > To: bio_bulletin_board at bioinformatics.org > Message-ID: <20050706144033.72298.qmail at web31501.mail.mud.yahoo.com> > Content-Type: text/plain; charset=iso-8859-1 > > Hi all > > I need to convert some chemical molecules which are in > .mol2 format to PDB format. When i try to do so using > Insight what i find is that bond information is lost. > > Can anybody suggest me a way for converting .mol2 > format to PDB format so that the bond information is > not lost. > > Thanks > Subhash > > > > > > > __________________________________________________________ > Free antispam, antivirus and 1GB to save all your messages > Only in Yahoo! Mail: http://in.mail.yahoo.com > > > ------------------------------ > > Message: 2 > Date: Wed, 06 Jul 2005 16:59:58 +0200 > From: Jan-Christoph Westermann > Subject: Re: [BiO BB] Mol2 to PDB > To: "The general forum at Bioinformatics.Org " > > Message-ID: <42CBF1EE.4060401 at sgi1.chemie.uni-hamburg.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Subhash Agarwal schrieb: > > Hi all > > > > I need to convert some chemical molecules which are in > > .mol2 format to PDB format. When i try to do so using > > Insight what i find is that bond information is lost. > > > > Can anybody suggest me a way for converting .mol2 > > format to PDB format so that the bond information is > > not lost. > > Try Open Babel. > http://openbabel.sourceforge.net/ > > HTH, > jcw > > > ------------------------------ > > _______________________________________________ > 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 9, Issue 3 > ************************************************ > -- E.Elavazhagan 09444332083 -------------- next part -------------- An HTML attachment was scrubbed... URL: From dmnunif at charter.net Mon Jul 11 17:01:32 2005 From: dmnunif at charter.net (D. Norris) Date: Mon, 11 Jul 2005 16:01:32 -0500 Subject: [BiO BB] Thiol/Disulfide Environmental Energy Exchange Code References: <002a01c58332$72739cb0$3382c418@VALUED4DA88152> <959075805070808566c9771e7@mail.gmail.com> Message-ID: <000701c5865b$b79d6a60$6ef19f18@VALUED4DA88152> Debarshi Roy: Sorry, we at Unifinium Ltd. can not answer your question; however, I doubt that a course is available although there should be one !! ----- Original Message ----- From: "debarshi roy" To: "The general forum at Bioinformatics.Org" Sent: Friday, July 08, 2005 10:56 AM Subject: Re: [BiO BB] Thiol/Disulfide Environmental Energy Exchange Code Hello, I would like to know if there is any online free course`available in Bioinformatics for the iernational students in USA? The course offered by Bitmap is purely for US citizens. Please inform me. Thanks Debarshi Roy On 7/7/05, D. Norris wrote: > > To Those Interested In Mechanistically How A Messenger Chemical Group or > Energy State Is Encoded Into Information In Biological Systems (i.e., > Viruses, Whole Cells, and Multicellular Organisms): > > After over 40 years of systems-biology research on the unifying dynamic > qualitative and quantitative mechanistic means of the transduction of > messenger chemical groups and energy states into information in biological > systems, the scientists at Unifinium Ltd have solidly confirmed repeatedly > in peer-reviewed published papers that the unifying mechanism is Thiol > (-SH) > / Disulfide (-S-S-) Exchange Protein Biophysics. The necessary unifying > messenger (UM) is sulfur exchange (electro) chemistry; and -SH, its > derivatives, and its redox couple, i.e., -S-S-, are the specific means by > which the UM is used to create the qualitative and quantitative > bioinformation. Our pertinent original research findings were first > published in "Nature" in 1969; "Science" 1970; "Experientia" 1971; etc., > "Nature" in 1973, & 1975; etc.; "Bioelectrochem. Bioenerget.", in 1985; "J > Chem Ecol", in 1988; a chapter in the book "Functional Dynamics of > Phytophagous Insects", edited by Ananthakrishnan, published by Oxford & > IBH > Publishing, New Delhi, 1994; and reviewed extensively in a chapter in the > book, "Predators and Parasitoids" , edited by Koul and Dhaliwal, published > by Taylor & Francis, London, in 2003. > A review recently was rejected by "Antioxidant & Redox Signaling" > especially > because it was "Too Broad". Our research has been broad in scope, and it > is > very broadly pertinent and valid. Have a read; it will not be a waste of > time for those who are really interested in energy transduction into > bioinformation in whole biological systems. dmn. > > P.S. If our research does not deal with bioinformatics, then we do not > mind > the "misfit". > _______________________________________________ > 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 jstroud at mbi.ucla.edu Wed Jul 13 02:43:03 2005 From: jstroud at mbi.ucla.edu (James Stroud) Date: Tue, 12 Jul 2005 23:43:03 -0700 Subject: [BiO BB] electrostatic map of proteins In-Reply-To: References: Message-ID: <200507122343.03440.jstroud@mbi.ucla.edu> On Thursday 07 July 2005 01:19, Dan Bolser wrote: > On Wed, 6 Jul 2005, James Stroud wrote: > >Also, you may want to plunk down the $500 for delphi from the Honig lab. I > >understand this is the best PB solver around. If you get it, check this > > page out: > > > >http://keres.colorado.edu/howto/delphi-surface-pymol.html > > Any screen shots :) > Sorry it took so long to write. I've been gone since Thurs. because I got married this weekend and just got email up at our house--I have not been at work since last Wed. Its kind of late Tue. night, so I'll try to put up screen shots later tomorrow (Wed.). But, let me say that the results are magificient. You will see what I mean. James -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com/ From golharam at umdnj.edu Wed Jul 13 15:20:19 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed, 13 Jul 2005 15:20:19 -0400 Subject: [BiO BB] BLAST and PVM Message-ID: <000001c587df$e82e1c80$e6028a0a@GOLHARMOBILE1> Is anyone using BLAST with PVM (Parallel Virtual Machine)? If so, I have some questions relating to your implementation that I would like to ask. Thanks, ----- Ryan Golhar Computational Biologist The Informatics Institute at The University of Medicine & Dentistry of NJ Email: golharam at umdnj.edu From mayagao at gmail.com Wed Jul 13 13:21:45 2005 From: mayagao at gmail.com (Gao Zhang) Date: Wed, 13 Jul 2005 10:21:45 -0700 Subject: [BiO BB] generate random motifs Message-ID: <7beac6a050713102159db9c72@mail.gmail.com> Hi all, I need some help to generate random motifs. The goal is to generate a random motif of width w. Each position will have a dominant letter with probability around 0.85. I know there is python module TAMO ( http://jura.wi.mit.edu/fraenkel/TAMO/documentation/TAMO.MotifTools.html#Motif-emit ) which can do this job. Can anybody know how to do this using Perl/Bioperl? Thank you very much and look forward to your reply! Best Regards, Maya -------------- next part -------------- An HTML attachment was scrubbed... URL: From x.sole at ico.scs.es Thu Jul 14 09:24:28 2005 From: x.sole at ico.scs.es (Sole Acha, Xavi) Date: Thu, 14 Jul 2005 15:24:28 +0200 Subject: [BiO BB] generate random motifs Message-ID: <5FF3F11444E3A9439191AA1EDCB69A1721D204@icosrvmail01.ICO.SCS.local> Hi, Perhaps this isn't the most straight way of doing it, but If you connect Perl with the statistical software R you could generate this random motifs you mention. R can also be called in batch mode from Perl or other scripting languages such as Python or PHP (via a "system" command or something similar). Hope this helps, Xavi. -----Mensaje original----- De: bio_bulletin_board-bounces+x.sole=ico.scs.es at bioinformatics.org [mailto:bio_bulletin_board-bounces+x.sole=ico.scs.es at bioinformatics.org] En nombre de Gao Zhang Enviado el: dimecres, 13 / juliol / 2005 19:22 Para: bio_bulletin_board at bioinformatics.org Asunto: [BiO BB] generate random motifs Hi all, I need some help to generate random motifs. The goal is to generate a random motif of width w. Each position will have a dominant letter with probability around 0.85. I know there is python module TAMO (http://jura.wi.mit.edu/fraenkel/TAMO/documentation/TAMO.MotifTools.html #Motif-emit ) which can do this job. Can anybody know how to do this using Perl/Bioperl? Thank you very much and look forward to your reply! Best Regards, Maya -------------- next part -------------- An HTML attachment was scrubbed... URL: From x.sole at ico.scs.es Thu Jul 14 10:47:58 2005 From: x.sole at ico.scs.es (Sole Acha, Xavi) Date: Thu, 14 Jul 2005 16:47:58 +0200 Subject: [BiO BB] Course on proteomics analysis: early registration extended Message-ID: <5FF3F11444E3A9439191AA1EDCB69A1721D21A@icosrvmail01.ICO.SCS.local> Apologies if you receive this more than once. --------------------------------------------- Course on STATISTICAL ANALYSIS OF PROTEOMICS DATA finding proteomic biomarkers for diagnosis and prognosis with Mass Spectrometry Barcelona, September 14th-16th 2005 -------------------------------------------------------------- REGISTRATION OPEN: Early registration extended until July 29th -------------------------------------------------------------- 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 boris.steipe at utoronto.ca Thu Jul 14 11:38:52 2005 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Thu, 14 Jul 2005 11:38:52 -0400 Subject: [BiO BB] generate random motifs In-Reply-To: <7beac6a050713102159db9c72@mail.gmail.com> Message-ID: <610BD907-F47D-11D9-B185-000A9577512E@utoronto.ca> Maya, You had asked me whether some code I had posted here in March can be adapted for your purpose (http://bioinformatics.org/pipermail/bio_bulletin_board/2005-March/ 002379.html). I have attached the adapted version below. Just a little programming fun on a hot summer Thursday morning in Toronto. I hope this helps. Just edit the definitions of motif and alphabet for your purposes. This is what I consider "teaching code" i.e. with an emphasis to demonstrate _how_ something can be done, with the newcomer in mind; especially if you want to go in and change things for your own purpose. Perl has many constructs to write something like this much more concisely, but that's not the point here. Have fun, Boris On Wednesday, Jul 13, 2005, at 13:21 America/Montreal, Gao Zhang wrote: > Hi all, > ? > I need some help to generate random motifs. The goal is to > generate?a?random?motif?of?width?w.??Each?position?will > have?a?dominant?letter?with?probability?around?0.85. > ? > I know there is python module TAMO > (http://jura.wi.mit.edu/fraenkel/TAMO/documentation/ > TAMO.MotifTools.html#Motif-emit ) > which can do this job. > ? > Can anybody know how to do this using Perl/Bioperl? > ? > Thank you very much and look forward to your reply! > ? > Best Regards, > ?? Maya > #!/usr/bin/perl # randommotifs.pl # # This program generates randomized instances of pseudomotifs, i.e. # sequences that are obtained by adding "noise", according to a specified # model to a consensus sequence. To keep this reasonably general, we # proceed through the following steps: # # Define consensus motif and alphabet # For the required number of repetitions # For each position in motif # Define an appropriate probability distribution over the alphabet # Produce a character according to the distribution # ... # ... # # The probability distributions are generated to produce a consensus character # with a particular "consensus probability" and all other characters # with equal probabilites (the noise). This is defined in a single subroutine # so it is straightforward to change this for a different model of noise # (e.g. increase the probabilities for "similar" characters). It's easy # to become creative here and incorporate (biological) knowledge into the # noise-model. # # Probablities are then converted into cumulative intervals to chose a # particular character: # # Eg: Probabilities A: 0.4, C: 0.3, G: 0.2, T: 0.1 # Intervals A: 0.4 C: 0.7, G: 0.9, T: 1.0 # # This example can be pictured as # # 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 # +----+----+----+----+----+----+----+----+----+----+ # | A | C | G | T | # +----+----+----+----+----+----+----+----+----+----+ # # .. now all we need to do is generate a random number between 0 and 1 # and see in which interval it falls. This then points to the character to be # written to output. # # B. Steipe, July 2005. Public domain code. # ===================================================================== use strict; use warnings; my $N_Sequences = 100; # Number of sequences to be generated my @Motif = split(//,'TTGACATATAAT'); # This example is simply a concatenation # of the -35 and -10 consensus elements # of prokaryotic promoters; replace with # whatever ... my @Alphabet = split(//,'ACGT'); # Nucleotides; replace with whatever ... my $P_Consensus = 0.85; # Replace with whatever ... # ====== Globals ========================== my @Probabilities; # Stores the probability of each character # ====== Program ========================== for (my $i=0; $i < $N_Sequences; $i++) { for (my $j=0; $j < scalar(@Motif); $j++) { loadConsensusCharacter($Motif[$j]); # Load the character for this position addNoiseToDistribution(); # Modify probabilities according to noise model convertToIntervals(); print(getRandomCharacter(rand(1.0))); # Output character } print "\n"; } exit(); # ====== Subroutines ======================= # sub loadConsensusCharacter { my ($char) = @_; my $Found = 'FALSE'; for (my $i=0; $i < scalar(@Alphabet); $i++) { if ( $char eq $Alphabet[$i]) { # found character in i_th position in Alphabet $Probabilities[$i] = 1.0; $Found = 'TRUE'; } else { $Probabilities[$i] = 0.0; } } if ($Found eq 'FALSE') { die("Panic: Motif-Character\"$char\" was not found in Alphabet. Aborting.\n"); } return(); } # ========================================== sub addNoiseToDistribution { # This implements a very simple noise model: # We work on an array in which one element is 1.0 and # all others are 0.0. The element with 1.0 has the same # index as the consensus character in the Alphabet. # # We change that value to the consensus probability and # we distribute the remaining probability equally among # all other elements. # # It should be straightforward to implement more elaborate # noise models, or use a position specific scoring matrix # or something else here. my $P_NonConsensus = (1.0-$P_Consensus) / (scalar(@Alphabet) - 1); for (my $i=0; $i < scalar(@Probabilities); $i++) { if ( $Probabilities[$i] == 1.0 ) { # ... this is the consensus character $Probabilities[$i] = $P_Consensus; } else { $Probabilities[$i] = $P_NonConsensus; } } return(); } # ========================================== sub convertToIntervals { my $Sum = 0; # Convert the values of the probabilities array to the top boundaries # of intervals having widths proportional to their relative frequency. # Numbers range from 0 to 1.0 ... for (my $i=1; $i < scalar(@Probabilities); $i++) { $Probabilities[$i] += $Probabilities[$i-1]; } return(); } # ========================================== sub getRandomCharacter { my ($RandomNumber) = @_; my $i=0; # Test which interval contains the RandomNumber ... # The index of the interval points to the Event we should choose. for ($i=0; $i < scalar(@Probabilities); $i++) { if ($Probabilities[$i] > $RandomNumber) { last; } } return($Alphabet[$i]); } From vetdebarshi at gmail.com Thu Jul 14 21:07:08 2005 From: vetdebarshi at gmail.com (debarshi roy) Date: Thu, 14 Jul 2005 20:07:08 -0500 Subject: [BiO BB] Looking for research assistanceship in Bioinformatics Message-ID: <9590758050714180742753427@mail.gmail.com> Hello Everybody, I am an International student, doing MS in Wichita State University, KS. I have started working in a bioinformatics lab in my university, but the problem is that there is no funding in my university. I am looking for somewhere in USA where I can get funding in this subject for the fall ' 05 session or the spring ' 06 session at least. Please reply , if you have any such information in this matter. Thanks. Debarshi Roy From mkgovindis at yahoo.com Fri Jul 15 07:00:10 2005 From: mkgovindis at yahoo.com (govind mk) Date: Fri, 15 Jul 2005 04:00:10 -0700 (PDT) Subject: [BiO BB] Re: Apple Mac OS X server In-Reply-To: <20050627063317.15575.qmail@webmail29.rediffmail.com> Message-ID: <20050715110011.93369.qmail@web54501.mail.yahoo.com> Hi all, We are in the process of procuring a server and need to evaluate the feasibility of the Apple Mac OS X server (PowerPC G5 processor) as a platform for running bioinformatics applications. I have had a look at the website http://www.apple.com/science/software/lifescience.html. I would like to know if there has been a specific problem anyone has experienced with regards to installing and executing general bioinformatics tools like (BLAST,HMMER,BLAT, Bioperl,Emboss rasmol etc..) and would also be happy if one could provide a comparison between Linux and Mac server. Thankyou, Regards, Govind __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From phoebe at deakin.edu.au Fri Jul 15 08:06:42 2005 From: phoebe at deakin.edu.au (Phoebe Chen) Date: Fri, 15 Jul 2005 22:06:42 +1000 Subject: [BiO BB] Final CFP (Deadline Extended): APBC2006 Message-ID: <1121429202.42d7a6d200e68@mail.deakin.edu.au> ================================================================ Due to many requests, the submission deadline has been extended to July 22nd 2005 !!! ================================================================ The Fourth Asia-Pacific Bioinformatics Conference Taipei, Taiwan 13-16 February 2006 Conference Web site: http://binfo.ym.edu.tw/apbc2006/ On line Submission Web site at: https://msrcmt.research.microsoft.com/APBC2006/CallForPapers.aspx =========================================================================== The Asia-Pacific Bioinformatics Conference series is an annual forum for exploring research, development, and applications in bioinformatics. The 4th Asia-Pacific Bioinformatics Conference, APBC2006, will be held in Taipei, Taiwan. High-throughput sequencing and functional genomics technologies have given us a human genome sequence and have enabled large-scale genotyping and gene expression profiling of human populations. Databases containing large numbers of sequences, polymorphisms, and gene expression profiles of normal and diseased tissues in different clinical states are rapidly being generated for human and model organisms. Bioinformatics is thus rapidly growing in importance in the understanding of the interplay between genes and proteins, in the analysis the genetic variability of species, etc. The aim of this conference is to bring together researchers, professionals, and industrial practitioners for interaction and exchange of knowledge and ideas. We invite submissions that address conceptual and practical issues of bioinformatics. Topics of Interest Papers are solicited on, but not limited to, the following topics: ?Novel Methods and Applications in Bioinformatics ?Data Mining & Statistical Modeling of Biological Data ?Computational Analysis of Biological Data ?Modeling and Simulation of Biological Processes ?Visualization of Biological Processes and Data ?Management, Migration, and Integration of Biological Databases ?Access, Indexing, and Search in Biological Databases ?Pathways and Systems Biology ?Structural Bioinformatics ?Population and Statistical Genetics ?Comparative Genomics ?Evolutionary Biology IMPORTANT DATES Full Paper Submission Deadline July 15, 2005 (Extended to 22 July 2005) Notification of Paper Acceptance Aug 20, 2005 Tutorial proposals Aug 25, 2005 Camera Ready Papers Due Sep 10, 2005 Author Registration Sep 10, 2005 Poster & demo proposals Sep 20 2005 Conference Feb 13 2006 ~ Feb 16 2006 GENERAL CO-CHAIRS Yi-Ping Phoebe Chen (Deakin University) Wen-Hsiung Li (The University of Chicago) Limsoon Wong (Institute for Infocomm Research) PROGRAM COMMITTEE CO-CHAIRS Tao Jiang, University of California ?Riverside Ueng-Cheng Yang, National Yang-Ming University PROGRAM COMMITTEE Tatsuya Akutsu (Kyoto University) Vineet Bafna (University of California ?San Diego) Paola Bonizzoni (University of Milano-Bicocca) David Bryant (McGill University/Niversity of Auckland) Kun-Mao Chao (National Taiwan University) Francis Chin (Hong-Kong University) Ross Coppel (Monash University) Michael Cummings (University of Maryland) Bhaskar DasGupta (University of Illinois ?Chicago) Nadia El-Mabrouk (University of Montreal) Janice Glasgow (Queens University) Sridhar Hannenhalli (University of Pennsylvania) Wen-Lian Hsu (Academia Sinica) Haiyan Huang (University of California ?Berkeley) Ming-Jing Hwang (Academia Sinica) John Kececioglu (University of Arizona) Chris Langmead (Carnegie Mellon University) Sang-Yup Lee (Korea Adv. Institute of Sci. & Technology) Jinyan Li (Institute for Infocomm Research) Jing Li (Case Western Reserve University) Guohui Lin (University of Alberta) Stefano Lonardi (University of California ?Riverside) Horng-Shing Lu (National Chao-Tung University) Bin Ma (University of Western Ontario) Shinichi Morishita (University of Tokyo) Laxmi Parida ( IBM, T.J. Watson Research Center) Kunsoo Park (Seoul National University) Christian Pedersen (University of Aarhus) Alexander Schliep (Max Planck Institute for Mol. Genetics) Shoba Ranganathan (Macquarie University) Christian Schoenbach (RIKEN) Larry Ruzzo (University of Washington) Lusheng Wang (City University of Hong-Kong) Wei Wang (University of North Carolina ?Chapel Hill) Eric Xing (Carnegie Mellon University) Michael Zhang (Cold Spring Harbor Laboratory) Yang Zhong (Fudan University) Xianghong Zhou (University of Southern California) ORGANIZATION COMMITTEE CO-CHAIRS Jorng-Tzong Horng (National Central University) Cheng-Yan Kao (National Taiwan University) SUBMISSION GUIDELINES APBC2006 invites high-quality original papers on any topic related to Bioinformatics. Papers should be no more than 10 pages in length conforming to the formatting instructions for the series Advances in Bioinformatics & Computational Biology (instructions available at the APBC2006 website). Each paper will be fully refereed by an international program committee. Papers will be judged on originality, significance, correctness, and clarity. Authors should submit one copy of a PDF or PS file to APBC2006 Paper Submission Website. The full paper must be submitted by 15 July 2005. The proceedings will be published as a volume in the series Advances in Bioinformatics & Computational Biology by Imperial College Press. Expanded version of the best papers will be invited for publication in the Journal of Bioinformatics and Computational Biology. To publish the paper in the conference, one of the authors needs to register for and present at the conference. From cdwan at bioteam.net Fri Jul 15 09:31:15 2005 From: cdwan at bioteam.net (Christopher Dwan) Date: Fri, 15 Jul 2005 09:31:15 -0400 Subject: [BiO BB] Re: Apple Mac OS X server In-Reply-To: <20050715110011.93369.qmail@web54501.mail.yahoo.com> References: <20050715110011.93369.qmail@web54501.mail.yahoo.com> Message-ID: <8825B8F5-C584-4D56-ADBF-5F4A871F0E28@bioteam.net> Disclosure: My company sells a piece of software which installs and configures a large number of bioinformatics apps under a web portal. The majority of installations of our software are on Apple XServes. We haven't had any trouble with the open source tools on OS X. The specific ones you mention all work fine, out of the box. Some commercial and closed source tools have been slow to provide binaries for Apple, but they're coming along now. The Bioinformatics Benchmark Suite is a decent tool for benchmarking systems on a popular set of tools in a common set of use cases (http://www.scalableinformatics.com/metadot/index.pl?iid=2194). My experience has been that benchmarks need to be tuned to the specific use case, or else they're hopelessly vague. You will get wildly different results depending on whether you need response time or throughput, HMMER or BLASTN, etc. -Chris Dwan The BioTeam On Jul 15, 2005, at 7:00 AM, govind mk wrote: > > Hi all, > > We are in the process of procuring a server and need > to evaluate the feasibility of the Apple Mac OS X > server (PowerPC G5 processor) as a platform for > running bioinformatics applications. > > I have had a look at the website > http://www.apple.com/science/software/lifescience.html. > > I would like to know if there has been a specific > problem anyone has experienced with regards to > installing and executing general bioinformatics tools > like (BLAST,HMMER,BLAT, Bioperl,Emboss rasmol etc..) > and would also be happy if one could provide a > comparison between Linux and Mac server. > > Thankyou, > > Regards, > Govind > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From marty.gollery at gmail.com Fri Jul 15 12:37:09 2005 From: marty.gollery at gmail.com (Martin Gollery) Date: Fri, 15 Jul 2005 09:37:09 -0700 Subject: [BiO BB] Re: Apple Mac OS X server In-Reply-To: <20050715110011.93369.qmail@web54501.mail.yahoo.com> References: <20050627063317.15575.qmail@webmail29.rediffmail.com> <20050715110011.93369.qmail@web54501.mail.yahoo.com> Message-ID: Hi Govind, I have run all of those apps on a G5 except for rasmol. The HMMer code in particular runs very quickly due to the altivec optimization. A dual G5 runs HMMer faster than a quad SGI Tezro, and costs 90% less! Marty On 7/15/05, govind mk wrote: > > Hi all, > > We are in the process of procuring a server and need > to evaluate the feasibility of the Apple Mac OS X > server (PowerPC G5 processor) as a platform for > running bioinformatics applications. > > I have had a look at the website > http://www.apple.com/science/software/lifescience.html. > > I would like to know if there has been a specific > problem anyone has experienced with regards to > installing and executing general bioinformatics tools > like (BLAST,HMMER,BLAT, Bioperl,Emboss rasmol etc..) > and would also be happy if one could provide a > comparison between Linux and Mac server. > > Thankyou, > > Regards, > Govind > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > 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 pmr at ebi.ac.uk Fri Jul 15 12:56:25 2005 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 15 Jul 2005 17:56:25 +0100 Subject: [BiO BB] Re: Apple Mac OS X server In-Reply-To: <20050715110011.93369.qmail@web54501.mail.yahoo.com> References: <20050715110011.93369.qmail@web54501.mail.yahoo.com> Message-ID: <42D7EAB9.5040401@ebi.ac.uk> govind mk wrote: > I would like to know if there has been a specific > problem anyone has experienced with regards to > installing and executing general bioinformatics tools > like (BLAST,HMMER,BLAT, Bioperl,Emboss rasmol etc..) > and would also be happy if one could provide a > comparison between Linux and Mac server. We support EMBOSS on MacOSX and various Linuxes. Should be no problem. If you have questions, just mail us on our (new) support address emboss-bug at emboss.open-bio.org regards, Peter Rice European Bioinformatics Institute From idonalds at blueprint.org Fri Jul 15 13:05:08 2005 From: idonalds at blueprint.org (Ian Donaldson) Date: Fri, 15 Jul 2005 13:05:08 -0400 Subject: [BiO BB] Re: Apple Mac OS X server In-Reply-To: Message-ID: Hi Govind You might want to check out the BioTeam web-site. They have a freely available OS X Bioinformatics Application installer. You might also ask them about optimizing apps for OSX and benchmark comparisons to Linux. http://rt.bioteam.net:8080/metadot/index.pl?iid=2377 Ian -----Original Message----- From: bio_bulletin_board-bounces+idonalds=blueprint.org at bioinformatics.org [mailto:bio_bulletin_board-bounces+idonalds=blueprint.org at bioinformatics .org]On Behalf Of Martin Gollery Sent: July 15, 2005 12:37 PM To: The general forum at Bioinformatics.Org Subject: Re: [BiO BB] Re: Apple Mac OS X server Hi Govind, I have run all of those apps on a G5 except for rasmol. The HMMer code in particular runs very quickly due to the altivec optimization. A dual G5 runs HMMer faster than a quad SGI Tezro, and costs 90% less! Marty On 7/15/05, govind mk wrote: > > Hi all, > > We are in the process of procuring a server and need > to evaluate the feasibility of the Apple Mac OS X > server (PowerPC G5 processor) as a platform for > running bioinformatics applications. > > I have had a look at the website > http://www.apple.com/science/software/lifescience.html. > > I would like to know if there has been a specific > problem anyone has experienced with regards to > installing and executing general bioinformatics tools > like (BLAST,HMMER,BLAT, Bioperl,Emboss rasmol etc..) > and would also be happy if one could provide a > comparison between Linux and Mac server. > > Thankyou, > > Regards, > Govind > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > 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 ----------- _______________________________________________ Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From mayagao at gmail.com Fri Jul 15 13:32:32 2005 From: mayagao at gmail.com (Gao Zhang) Date: Fri, 15 Jul 2005 10:32:32 -0700 Subject: [BiO BB] A question about replacing a substring using Bioperl In-Reply-To: References: <7beac6a05071508535feea867@mail.gmail.com> Message-ID: <7beac6a0507151032148bd615@mail.gmail.com> Dear all, I have a txt file which stores 20 short DNA sequences and the length of each is 8, let's call it A. Meanwhile, I have another txt file which owns 100 long DNA sequences and the length of each is 200, let's call it B. Then, I want to replace a substring of each sequence in B with each one in A. The replacement starting site could be specified as you want(such as starting at position 1 for the first sequence in B, 10th for the 2nd sequence in B, 20th for the 3rd, until 190th for the 20th in B ) or picked by the program randomly. I am pretty sure substr(string,index,length,replacement string) can finish a part of this work. But I have limited experience of using Perl to manipulate two files. Can anybody give me some suggestions? Thank you very much and look forward to your reply! Best Regards, Maya -------------- next part -------------- An HTML attachment was scrubbed... URL: From dmnunif at charter.net Sat Jul 16 17:35:50 2005 From: dmnunif at charter.net (D. Norris) Date: Sat, 16 Jul 2005 16:35:50 -0500 Subject: [BiO BB] Website for Unifinium Ltd Bioinformatics Info Message-ID: <000f01c58a4e$576312c0$7c7eb118@VALUED4DA88152> Our URL is: http://www.plantcarebyunifinium.com/bioinformaticsbyunifiniumltd/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From Sudhindra.Gadagkar at notes.udayton.edu Sun Jul 17 11:09:25 2005 From: Sudhindra.Gadagkar at notes.udayton.edu (Sudhindra.Gadagkar at notes.udayton.edu) Date: Sun, 17 Jul 2005 11:09:25 -0400 Subject: [BiO BB] Looking for research assistanceship in Bioinformatics In-Reply-To: <9590758050714180742753427@mail.gmail.com> Message-ID: Hello Debashri, What is the lack of funding for? To pay your living expenses as an RA or to fund research in your lab? I am assuming you want to pursue a graduate degree. In our university, all graduate students have the opportunity to meet reasonable living expenses by means of a TA-ship. Please have a look at my website below (that needs some updating) and if you find the kind of research I do interesting, send me your resume and we can then talk. Let me know Dr. 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 Web: http://academic.udayton.edu/sudhindraGadagkar/ ---------------------------------------------------------------------------- debarshi roy Sent by: bio_bulletin_board-bounces+sudhindra.gadagkar=notes.udayton.edu at bioinformatics.org 07/14/2005 09:07 PM Please respond to debarshi roy ; Please respond to "The general forum at Bioinformatics.Org" To BiO_Bulletin_Board at bioinformatics.org cc Subject [BiO BB] Looking for research assistanceship in Bioinformatics Hello Everybody, I am an International student, doing MS in Wichita State University, KS. I have started working in a bioinformatics lab in my university, but the problem is that there is no funding in my university. I am looking for somewhere in USA where I can get funding in this subject for the fall ' 05 session or the spring ' 06 session at least. Please reply , if you have any such information in this matter. Thanks. Debarshi Roy _______________________________________________ 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 rajkumar.bondugula at gmail.com Sun Jul 17 21:13:37 2005 From: rajkumar.bondugula at gmail.com (Raj) Date: Sun, 17 Jul 2005 20:13:37 -0500 Subject: [BiO BB] BLOSUM matrices Message-ID: <353b2b105071718134d026cb9@mail.gmail.com> Hi all, I was wondering if there are latest BLOSUM matrices somewhere. The matrices in NCBI website are like 8 years old. May be my understanding is limited but, do the scoring matrices change as new structures are being solved and added to the database? Regards, Raj =================================== Rajkumar Bondugula Digital Biology Laboratory University of Missouri-Columbia http://digbio.missouri.edu/~raj =================================== From idoerg at burnham.org Sun Jul 17 22:41:13 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Sun, 17 Jul 2005 19:41:13 -0700 Subject: [BiO BB] BLOSUM matrices In-Reply-To: <353b2b105071718134d026cb9@mail.gmail.com> Message-ID: Hi Raj, Actually, the BLOSUM matrices are constructed based on sequence alignments, not on structures. More specifically, they are based on the alignments in the BLOCKS database. http://blocks.fhcrc.org/ However, going there I could not find updated BLOSUM matrices, although the BLOCKS is being updated. You should probably email the BLOCKS folks for updated matrices. It would be interesting to see if there is any significant difference between old and new BLOSUM matrices. Although there is an ongoing explosion in the number of sequences that we have, the statistics of teh composition of aligned positions doe snot seem to have changed appreciably. 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 On Sun, 17 Jul 2005, Raj wrote: > Hi all, > I was wondering if there are latest BLOSUM matrices somewhere. The > matrices in NCBI website are like 8 years old. May be my understanding > is limited but, do the scoring matrices change as new structures are > being solved and added to the database? > > Regards, > Raj > > =================================== > Rajkumar Bondugula > Digital Biology Laboratory > University of Missouri-Columbia > http://digbio.missouri.edu/~raj > =================================== > _______________________________________________ > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From mayagao1999 at yahoo.com Mon Jul 18 17:06:10 2005 From: mayagao1999 at yahoo.com (Alex Zhang) Date: Mon, 18 Jul 2005 14:06:10 -0700 (PDT) Subject: [BiO BB] how to work on two txt files simultaneously by handle corresponding lines from each file Message-ID: <20050718210610.18944.qmail@web53509.mail.yahoo.com> Dear All, Sorry to bother you again. I have two txt files to handle. One is "short_sequences" and the other one is "long_sequences". The "short_sequences" holds 100 short sequences (8 nucleotide long) and 100 long sequences (200 nucleotide long) in the "long_sequence". For example, the first short sequence is "TTGACATA" and the first long sequence is "GAATCATATATTAGTCTCCACATACTCCGTTCGTGACCCATTACCCTTTCGGGAGA GCCACAGCAACTGTAGATCTCGAAGTTGACAGGGGCAACTAGAGGCCTCAGAATTCT CACTCTTGAGGAGAGAAGTCTAAGACCTACAGTATGGTCGGGTTAGTTTTTGTTCCGTC GAACCTTGGACTAACCACTGTCTGGATA". Basically, I want to generate a random position as a starting site to replace a substring in the long sequence with a short sequence. In this example, we can choose a starting site as 5th nucleotide in the long sequence, after replacing using "TTGACATA", the replaced long sequence is "GAATTTGACATAAGTCTCCACATACTCCGTTCGTGACCCATTACCCTTTCGGGAGA GCCACAGCAACTGTAGATCTCGAAGTTGACAGGGGCAACTAGAGGCCTCAGAATTCT CACTCTTGAGGAGAGAAGTCTAAGACCTACAGTATGGTCGGGTTAGTTTTTGTTCCGTC GAACCTTGGACTAACCACTGTCTGGATA". Then I want replace the 2nd long sequence with the 2nd short sequence and then repeat this over and over again until the last long sequence is reached and replaced. I think the only problem is that the starting site should not be larger than 193. Otherwise, there are not enough nucleotides in the long sequence for replacement. Furthurmore, I want to keep track the starting replacement site for each long sequence. I am copying my code in the below. ****************************************** use strict; use warnings; my (@short, @long, $offset); # the 'short' array will hold the short #sequences while 'long' array the long sequences open(FILE1, '<', "short_sequences.txt") || die "Can't open short_sequences.txt: $!\n"; while(){ chomp; push(@short, $_); } close FILE1; #Close the file open(FILE2, '<', "long_sequences.txt") || die "Can't open long_sequences.txt: $!\n"; while(){ chomp; push(@long, $_); } close FILE2; #Close the file # replacement foreach my $short(@short){ foreach my $long(@long){ $offset = int(rand(length($long)%193)); substr($long,$offset,length($short),$short); printf "%3d", $offset+1; print "\n", $long, "\n"; } } ******************************************** But I just realized that there is a problem for the two loops. The problem is that each short sequence will be used to replace all long sequences not the corresponding one. So I seek your suggestions on how to handle two files simultaneously for my case. Thank you very much and look forward to your reply! Best Regards, Alex __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From elena at cs.vu.nl Tue Jul 19 03:58:25 2005 From: elena at cs.vu.nl (Marchiori Elena) Date: Tue, 19 Jul 2005 09:58:25 +0200 (GMT) Subject: [BiO BB] EvoBIO 2006 CFP Message-ID: --------------------------------------------------------------- Call for Papers EvoBIO2006 Fourth European Workshop on Evolutionary Computation and Machine Learning in Bioinformatics Budapest, Hungary http://evonet.lri.fr//eurogp2006/?page=evobio http://www.cs.vu.nl/~evobio/evobio06.html ---------------------------------------------------------------- EvoBIO covers research in all aspects of computational intelligence in bioinformatics and computational biology. The emphasis is on algorithms based on evolutionary computation, on neural networks and on other novel optimisation and machine learning methods, that address important problems in molecular biology, genomics and genetics, that are computationally efficient, and that have been implemented and tested in simulations and on real datasets. The goal of the workshop is to present recent research results, including significant work-in-progress, and to identify and explore directions of future research, besides stimulating closer interaction between members of this scientific community working on Bioinformatics. Each accepted paper will be presented orally at the workshop and printed in the proceedings published by Springer in the LNCS series. The accepted papers of the first, second, and third edition of EvoBIO were published in the Springer Verlag LNCS 2611, 3005, 3449, respectively. ****** Important Dates ****** Submission deadline: 4 November 2005 Notification of acceptance: 12 December 2005 Camera ready papers due: 9 January 2006 EvoBIO and Evo-events: 10-12 April 2006 ****** Program Chairs ****** Carlos Cotta ccottap at lcc.uma.es University of Malaga (Spain) Jason Moore Jason.h.moore at Dartmouth.edu Dartmouth College - CGL (USA) ****** Publicity Chair ****** Jagath C. Rajapakse asjagath at ntu.edu.sg Nanyang Technology University (Singapore) ****** Technical Committee ****** Dave Corne (general co-chair) (UK) Vincenzo Cutello (Italy) James Foster (USA) Elena Marchiori (general co-chair) (NL) Jason Moore (USA) Pablo Moscato (Australia) Ajit Narayanan (UK) Marylyn Ritchie (USA) Jagath Rajapakse (Singapore) From biopctgi at yahoo.es Wed Jul 20 11:19:29 2005 From: biopctgi at yahoo.es (Jose Maria Gonzalez Izarzugaza) Date: Wed, 20 Jul 2005 17:19:29 +0200 Subject: [BiO BB] how to work on two txt files simultaneously by handle corresponding lines from each file In-Reply-To: <20050718210610.18944.qmail@web53509.mail.yahoo.com> References: <20050718210610.18944.qmail@web53509.mail.yahoo.com> Message-ID: <42DE6B81.6030600@yahoo.es> Hello Alex, I think that what you want is to modify long1 with short1, long2 with short2 and so on. I recommed you to replace your 2 loops with this one. for ($seq=0;$seqDear All, > >Sorry to bother you again. > >I have two txt files to handle. One is >"short_sequences" and the other >one is "long_sequences". The "short_sequences" holds >100 short sequences (8 nucleotide long) and 100 long >sequences (200 nucleotide long) in the >"long_sequence". > >For example, the first short sequence is "TTGACATA" >and the first long sequence is >"GAATCATATATTAGTCTCCACATACTCCGTTCGTGACCCATTACCCTTTCGGGAGA >GCCACAGCAACTGTAGATCTCGAAGTTGACAGGGGCAACTAGAGGCCTCAGAATTCT >CACTCTTGAGGAGAGAAGTCTAAGACCTACAGTATGGTCGGGTTAGTTTTTGTTCCGTC >GAACCTTGGACTAACCACTGTCTGGATA". > >Basically, I want to generate a random position as a >starting site to replace a substring >in the long sequence with a short sequence. In this >example, we can choose a starting site >as 5th nucleotide in the long sequence, after >replacing using "TTGACATA", the replaced >long sequence is >"GAATTTGACATAAGTCTCCACATACTCCGTTCGTGACCCATTACCCTTTCGGGAGA >GCCACAGCAACTGTAGATCTCGAAGTTGACAGGGGCAACTAGAGGCCTCAGAATTCT >CACTCTTGAGGAGAGAAGTCTAAGACCTACAGTATGGTCGGGTTAGTTTTTGTTCCGTC >GAACCTTGGACTAACCACTGTCTGGATA". > >Then I want replace the 2nd long sequence with the 2nd >short sequence and then repeat this over and over >again until the last long sequence is reached and >replaced. I think the only problem is that the >starting site should not be larger than 193. >Otherwise, there are >not enough nucleotides in the long sequence for >replacement. > >Furthurmore, I want to keep track the starting >replacement site for each long sequence. > > >I am copying my code in the below. >****************************************** >use strict; >use warnings; > >my (@short, @long, $offset); # the 'short' array will >hold the short > #sequences while 'long' >array the long sequences > >open(FILE1, '<', "short_sequences.txt") || die "Can't >open short_sequences.txt: $!\n"; >while(){ > chomp; > push(@short, $_); >} >close FILE1; #Close the file > >open(FILE2, '<', "long_sequences.txt") || die "Can't >open long_sequences.txt: $!\n"; >while(){ > chomp; > push(@long, $_); >} >close FILE2; #Close the file > > ># replacement >foreach my $short(@short){ > foreach my $long(@long){ > $offset = int(rand(length($long)%193)); > substr($long,$offset,length($short),$short); > printf "%3d", $offset+1; > print "\n", $long, "\n"; > > } >} >******************************************** > >But I just realized that there is a problem for the >two >loops. The problem is that each short sequence will be >used to replace all long sequences not the >corresponding one. > >So I seek your suggestions on how to handle two files >simultaneously for my case. > >Thank you very much and look forward to your reply! > >Best Regards, > Alex > >__________________________________________________ >Do You Yahoo!? >Tired of spam? Yahoo! Mail has the best spam protection around >http://mail.yahoo.com >_______________________________________________ >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > From daniel.amelang at gmail.com Wed Jul 20 14:28:48 2005 From: daniel.amelang at gmail.com (Daniel Amelang) Date: Wed, 20 Jul 2005 11:28:48 -0700 Subject: [BiO BB] how to work on two txt files simultaneously by handle corresponding lines from each file In-Reply-To: <20050718210610.18944.qmail@web53509.mail.yahoo.com> References: <20050718210610.18944.qmail@web53509.mail.yahoo.com> Message-ID: Does anyone know why the bioperl mailing list messages show up on the bioinformatics bulletin board mailing list? Is there a misconfiguration of the bioperl list? Dan From jeff at bioinformatics.org Wed Jul 20 14:43:35 2005 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 20 Jul 2005 14:43:35 -0400 Subject: [BiO BB] how to work on two txt files simultaneously by handle corresponding lines from each file In-Reply-To: References: <20050718210610.18944.qmail@web53509.mail.yahoo.com> Message-ID: <42DE9B57.7020609@bioinformatics.org> It's probably a blind carbon copy (BCC). Jeff Daniel Amelang wrote: > Does anyone know why the bioperl mailing list messages show up on the > bioinformatics bulletin board mailing list? Is there a > misconfiguration of the bioperl list? > > Dan -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From rajkumar.bondugula at gmail.com Wed Jul 20 15:50:18 2005 From: rajkumar.bondugula at gmail.com (Raj) Date: Wed, 20 Jul 2005 14:50:18 -0500 Subject: [BiO BB] Orphan Protein Message-ID: <353b2b1050720125014981c20@mail.gmail.com> Hi all, I need some 'orphan proteins' to test my secondary structure prediction algorithm. By 'orphan protein', I mean those proteins that do not have significant sequence identity(>10%) with other known proteins. Does any one know of a pre-compiled list of orphan proteins? or can any one suggest me a method to generate a list. Thanks in advance. Raj From marty.gollery at gmail.com Wed Jul 20 16:11:10 2005 From: marty.gollery at gmail.com (Martin Gollery) Date: Wed, 20 Jul 2005 13:11:10 -0700 Subject: [BiO BB] Orphan Protein In-Reply-To: <353b2b1050720125014981c20@mail.gmail.com> References: <353b2b1050720125014981c20@mail.gmail.com> Message-ID: Yes, I have some that I have been working with- I will dump them to a webserver and then drop you a line as to where they are. Marty On 7/20/05, Raj wrote: > Hi all, > I need some 'orphan proteins' to test my secondary structure > prediction algorithm. By 'orphan protein', I mean those proteins that > do not have significant sequence identity(>10%) with other known > proteins. > > Does any one know of a pre-compiled list of orphan proteins? or > can any one suggest me a method to generate a list. > > > Thanks in advance. > Raj > _______________________________________________ > 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 mayagao1999 at yahoo.com Wed Jul 20 21:19:17 2005 From: mayagao1999 at yahoo.com (Alex Zhang) Date: Wed, 20 Jul 2005 18:19:17 -0700 (PDT) Subject: [BiO BB] how to work on two txt files simultaneously by handle corresponding lines from each file In-Reply-To: <42DE6B81.6030600@yahoo.es> Message-ID: <20050721011917.83066.qmail@web53508.mail.yahoo.com> Dear Jose, Thank you very much! Best Regards, Alex --- Jose Maria Gonzalez Izarzugaza wrote: > Hello Alex, > > I think that what you want is to modify long1 with > short1, long2 with > short2 and so on. > > I recommed you to replace your 2 loops with this > one. > > for ($seq=0;$seq $short=$short[$seq]; > $long=$long[$seq]; > $offset = int(rand(length($long)%193)); > substr($long,$offset,length($short),$short); > printf "%3d", $offset+1; > print "\n", $long, "\n"; > } > > Good Luck! > Txema > > > Alex Zhang wrote: > > >Dear All, > > > >Sorry to bother you again. > > > >I have two txt files to handle. One is > >"short_sequences" and the other > >one is "long_sequences". The "short_sequences" > holds > >100 short sequences (8 nucleotide long) and 100 > long > >sequences (200 nucleotide long) in the > >"long_sequence". > > > >For example, the first short sequence is "TTGACATA" > >and the first long sequence is > >"GAATCATATATTAGTCTCCACATACTCCGTTCGTGACCCATTACCCTTTCGGGAGA > >GCCACAGCAACTGTAGATCTCGAAGTTGACAGGGGCAACTAGAGGCCTCAGAATTCT > >CACTCTTGAGGAGAGAAGTCTAAGACCTACAGTATGGTCGGGTTAGTTTTTGTTCCGTC > >GAACCTTGGACTAACCACTGTCTGGATA". > > > >Basically, I want to generate a random position as > a > >starting site to replace a substring > >in the long sequence with a short sequence. In this > >example, we can choose a starting site > >as 5th nucleotide in the long sequence, after > >replacing using "TTGACATA", the replaced > >long sequence is > >"GAATTTGACATAAGTCTCCACATACTCCGTTCGTGACCCATTACCCTTTCGGGAGA > >GCCACAGCAACTGTAGATCTCGAAGTTGACAGGGGCAACTAGAGGCCTCAGAATTCT > >CACTCTTGAGGAGAGAAGTCTAAGACCTACAGTATGGTCGGGTTAGTTTTTGTTCCGTC > >GAACCTTGGACTAACCACTGTCTGGATA". > > > >Then I want replace the 2nd long sequence with the > 2nd > >short sequence and then repeat this over and over > >again until the last long sequence is reached and > >replaced. I think the only problem is that the > >starting site should not be larger than 193. > >Otherwise, there are > >not enough nucleotides in the long sequence for > >replacement. > > > >Furthurmore, I want to keep track the starting > >replacement site for each long sequence. > > > > > >I am copying my code in the below. > >****************************************** > >use strict; > >use warnings; > > > >my (@short, @long, $offset); # the 'short' array > will > >hold the short > > #sequences while 'long' > >array the long sequences > > > >open(FILE1, '<', "short_sequences.txt") || die > "Can't > >open short_sequences.txt: $!\n"; > >while(){ > > chomp; > > push(@short, $_); > >} > >close FILE1; #Close the file > > > >open(FILE2, '<', "long_sequences.txt") || die > "Can't > >open long_sequences.txt: $!\n"; > >while(){ > > chomp; > > push(@long, $_); > >} > >close FILE2; #Close the file > > > > > ># replacement > >foreach my $short(@short){ > > foreach my $long(@long){ > > $offset = int(rand(length($long)%193)); > > substr($long,$offset,length($short),$short); > > printf "%3d", $offset+1; > > print "\n", $long, "\n"; > > > > } > >} > >******************************************** > > > >But I just realized that there is a problem for the > >two > >loops. The problem is that each short sequence will > be > >used to replace all long sequences not the > >corresponding one. > > > >So I seek your suggestions on how to handle two > files > >simultaneously for my case. > > > >Thank you very much and look forward to your reply! > > > >Best Regards, > > Alex > > > >__________________________________________________ > >Do You Yahoo!? > >Tired of spam? Yahoo! Mail has the best spam > protection around > >http://mail.yahoo.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 > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From katia at cin.ufpe.br Thu Jul 21 09:34:53 2005 From: katia at cin.ufpe.br (=?ISO-8859-1?Q?=22Katia_S=2E_Guimar=E3es=22?=) Date: Thu, 21 Jul 2005 10:34:53 -0300 Subject: [BiO BB] Orphan Protein In-Reply-To: References: <353b2b1050720125014981c20@mail.gmail.com> Message-ID: <42DFA47D.4060908@cin.ufpe.br> Hi, mArtin, We are working on a program to do supersecondary structure prediction, and that site would interest us too, if you don?t mind. Many Thanks, Katia Guimaraes Martin Gollery wrote: >Yes, I have some that I have been working with- I will dump them to a >webserver and then drop you a line as to where they are. > >Marty > >On 7/20/05, Raj wrote: > > >>Hi all, >> I need some 'orphan proteins' to test my secondary structure >>prediction algorithm. By 'orphan protein', I mean those proteins that >>do not have significant sequence identity(>10%) with other known >>proteins. >> >> Does any one know of a pre-compiled list of orphan proteins? or >>can any one suggest me a method to generate a list. >> >> >>Thanks in advance. >>Raj >>_______________________________________________ >>Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> >> > > > > From biopctgi at yahoo.es Fri Jul 22 03:16:02 2005 From: biopctgi at yahoo.es (Jose Maria Gonzalez Izarzugaza) Date: Fri, 22 Jul 2005 09:16:02 +0200 Subject: [BiO BB] how to work on two txt files simultaneously by handle corresponding lines from each file In-Reply-To: <20050721192551.31293.qmail@web53501.mail.yahoo.com> References: <20050721192551.31293.qmail@web53501.mail.yahoo.com> Message-ID: <42E09D32.8020402@yahoo.es> Hello Alex, It is easy as pie. The idea: 1) First generate the library of posibilities (16) in an array named @library. 2) There should be another array name @already_used with the same amount of entries (At the beginning assign 1 to all entries, and when i-th element from @library is selected to be used in any group. [Think on it as a label 0->Used, 1->Not used for the same entry index.] 3) When you choose the element to be inserted in a group skip and repeat in case it has been already used (this is, the label is 0), if not, mark it as visited and copy it to your group array. The code (It is not debugged, it might contain errors, think of it as a very detailed pseudocode) #generate the library @library=qw(AA AC AT AG CA CC CG CT GA GC GG GT TA TC TG TT); #generate already used array for ($i=0;$i Dear Jose, > > Thank you very much for your suggestions! I also came up with the almost > same idea with yours. That was great and I appreciate it. > > Can I ask for another help from you on my question? > > . > > The thread is: > > (1)First,randomly select 4 pairs of nucleotides as the group A. > > For example, we randomly select 4 pairs of nucleotides, ??CA??, > ??TG??, ??CG??, and ??TC?? from 16 combinations of two nucleoties : > > AA,AC,AG,AT, > CA,CC,CG,CT, > GA,GC,GG,GT, > TA,TC,TG,TT > > > Then randomly select another 4 pairs of nucleotides, for instance, > like ??AA??,??CA??,??CT?? and ??TT?? as the group B. > > Any pair in group A should be different from the one in group B. > > (2)To create the motif binding site. Choose ??CA??, the first pair > from the group A with 85% probability or ??AA?? from the group B with > 15% probability to occupy the 1st position in the binding site, which > means that each pair in the group A will be the dominant pair compared > to the one in the group B. The sum of probabilities of corresponding > pairs in group A and B will be 1.00 (0.85+0.15=1.00). > > Repeat this for the next 3 positions and put 4 pairs of nucleotides > together, we will end up with a random binding motif like: > > CA --- 1st position > CC --- 2nd position > CG --- 3rd position > TC --- 4th position > > CACCCGTC----the 8 bp long binding motif site > > We also can form another group A like GG,GT,AT,CG and group > B like GA,AA,AC,CC. > > Then we can get a random motif like: GGAAATCG > > > (3)Repeat this to make another 99 binding motif sites. > > > > I had experience of generating 8 base-pair long indepent motif binding > sites with the probability of dominant nucleotide as 0.85. But I don't > know how to generate two groups of pairs of nucleotides which are not > identical. Thank you very much for suggestions! > > Alex > > > > The previous code is: > > ## $len = length of the sequence - 1 > $len = 2; > > ## $ar[i] letter in position i with probability $ap[i] > ## other letters have the same probability (in our case 0.05) > ## you have to build the arrays > $ar[0] = "T"; > $ap[0] = 0.85; > > $ar[1] = "C"; > $ap[1] = 0.85; > > $ar[2] = "A"; > $ap[2] = 0.85; > > for ($i=0;$i<=$len;$i++) { > > $ar_other[$i][0] = "A"; > $ar_other[$i][1] = "C"; > $ar_other[$i][2] = "G"; > > if ($ar[$i] eq "A") { > $ar_other[$i][0] = "T"; > } elsif ($ar[$i] eq "C") { > $ar_other[$i][1] = "T"; > } elsif ($ar[$i] eq "G") { > $ar_other[$i][2] = "T"; > } > > $p = rand(1); > #print > "$p"; > if ($p<(1-$ap[$i])) { > $frac = (1-$ap[$i])/3; > if ($p<(1-$ap[$i]-(2*$frac))) { > $ran_seq[$i] = $ar_other[$i][0]; > } elsif ($p<(1-$ap[$i]-$frac)) { > $ran_seq[$i] = $ar_other[$i][1]; > } else { > $ran_seq[$i] = $ar_other[$i][2]; > } > } else { > > $ran_seq[$i] = $ar[$i]; > > } > > } > > ## you have your sequence in the array @ran_seq > for ($i=0;$i<=$len;$i++) { > print "$ran_seq[$i] "; > } > print "\n"; > > > A overly longer code is: > > #!/usr/bin/perl > # randommotifs.pl > # > # This program > generates > randomized instances of pseudomotifs, i.e. > # sequences that are obtained by adding "noise", according to a > specified > # model to a consensus sequence. To keep this reasonably general, we > # proceed through the following steps: > # > # Define consensus motif and alphabet > # For the required number of repetitions > # For each position in motif > # Define an appropriate probability distribution over the > alphabet > # Produce a character according to the distribution > # ... > # ... > # > # The probability distributions are generated to produce a consensus > character > # with a particular "consensus probability" and all other characters > # with equal probabilites (the noise). This is defined in a single > subroutine > # so it is straightforward to change this for a different model of noise > # (e.g. increase the probabilities for "similar" characters). It's easy > # to become creative here and incorporate (biological) knowledge into > the > # noise-model. > # > # Probablities are then converted into cumulative intervals to chose a > # particular character: > # > # Eg: Probabilities A: 0.4, C: 0.3, G: 0.2, T: 0.1 > # Intervals A: 0.4 C: 0.7, G: 0.9, T: 1.0 > # > # This example can be pictured as > # > # 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 > # +----+----+----+----+----+---- > +----+----+----+----+ > # | A | C | G | T | > # +----+----+----+----+----+----+----+----+----+----+ > # > # .. now all we need to do is generate a random number between 0 and 1 > # and see in which interval it falls. This then points to the character > to be > # written to output. > # > # B. Steipe, July 2005. Public domain > code. > # ===================================================================== > > use strict; > use warnings; > > > my $N_Sequences = 100; # Number of sequences to be > generated > my @Motif = split(//,'TTGACATATAAT'); # This example is simply a > concatenation > # of the -35 and -10 consensus > elements > # of prokaryotic promoters; > replace with > # whatever ... > my @Alphabet = split(//,'ACGT'); # Nucleotides; replace with > whatever ... > my $P_Consensus = 0.85; # Replace with whatever ... > > # ====== Globals ========================== > my @Probabilities; # Stores the probability of each > character > # ====== Program ========================== > > > for (my $i=0; $i < $N_Sequences; $i++) { > for (my $j=0; $j < scalar(@Motif); $j++) { > > loadConsensusCharacter($Motif[$j]); # Load the character for > this position > addNoiseToDistribution(); # Modify probabilities > according to noise model > convertToIntervals(); > print(getRandomCharacter(rand(1.0))); # Output character > } > print "\n"; > } > > exit(); > > # ====== Subroutines ======================= > # > sub loadConsensusCharacter { > my ($char) = @_; > my $Found = 'FALSE'; > > for (my $i=0; $i < scalar(@Alphabet); $i++) { > if ( $char eq $Alphabet[$i]) { # found character in i_th > position in Alphabet > $Probabilities[$i] = 1.0; > $Found = 'TRUE'; > } else { > $Probabilities[$i] = 0.0; > } > } > if ($Found eq 'FALSE') { > die("Panic: Motif-Character\"$char\" was not found in Alphabet. > Aborting.\n"); > } > > return(); > } > > # ========================================== > sub addNoiseToDistribution { > > # This implements a very simple noise model: > # We work on an array in which one element is 1.0 and > # all others are 0.0. The element with 1.0 has the same > # index as the consensus character in the Alphabet. > # > # We change that value to the consensus probability and > # we distribute the remaining probability equally among > # all other elements. > # > # It should be straightforward to implement more elaborate > # noise models, or use a position specific scoring matrix > # or something else here. > > my $P_NonConsensus = ( 1.0-$P_Consensus) / (scalar(@Alphabet) - 1); > > for (my $i=0; $i < scalar(@Probabilities); $i++) { > if ( $Probabilities[$i] == 1.0 ) { # ... this is the consensus > character > $Probabilities[$i] = $P_Consensus; > } else { > $Probabilities[$i] = $P_NonConsensus; > } > } > > return(); > } > > # ========================================== > sub convertToIntervals { > > my $Sum = 0; > > # Convert the values of the probabilities array to the top > boundaries > # of intervals having widths proportional to their relative > frequency. > # Numbers range from 0 to 1.0 ... > > for (my $i=1; $i < scalar(@Probabilities); $i++) { > $Probabilities[$i] += $Probabilities[$i-1]; > } > > return(); > } > > # ========================================== > sub getRandomCharacter { > > my ($RandomNumber) = @_; > my $i=0; > > # Test which interval contains the RandomNumber ... > # The index of the interval points to the Event we should choose. > > for ($i=0; $i < scalar(@Probabilities); $i++) { > if ($Probabilities[$i] > $RandomNumber) { last; } > } > > return($Alphabet[$i]); > } > > */Jose Maria Gonzalez Izarzugaza /* wrote: > > Hello Alex, > > I think that what you want is to modify long1 with short1, long2 with > short2 and so on. > > I recommed you to replace your 2 loops with this one. > > for ($seq=0;$seq > $short=$short[$seq]; > $long=$long[$seq]; > $offset = int(rand(length($long)%193)); > substr($long,$offset,length($short),$short); > printf "%3d", $offset+1; > print "\n", $long, "\n"; > } > > Good Luck! > Txema > > > Alex Zhang wrote: > > >Dear All, > > > >Sorry to bother you again. > > > >I have two txt files to handle. One is > >"short_sequences" and the other > >one is "long_sequences". The "short_sequences" holds > >100 short sequences (8 nucleotide long) and 100 long > >sequences (200 nucleotide long) in the > >"long_sequence". > > > >For example, the first short sequence is "TTGACATA" > >and the first long sequence is > >"GAATCATATATTAGTCTCCACATACTCCGTTCGTGACCCATTACCCTTTCGGGAGA > >GCCACAGCAACTGTAGATCTCGAAGTTGACAGGGGCAACTAGAGGCCTCAGAATTCT > >CACTCTTGAGGAGAGAAGTCTAAGACCTACAGTATGGTCGGGTTAGTTTTTGTTCCGTC > >GAACCTTGGACTAACCACTGTCTGGATA". > > > >Basically, I want to generate a random position as a > >starting site to replace a substring > >in the long sequence with a short sequence. In this > >example, we can choose a starting site > >as 5th nucleotide in the long sequence, after > >replacing using "TTGACATA", the replaced > >long sequence is > >"GAATTTGACATAAGTCTCCACATACTCCGTTCGTGACCCATTACCCTTTCGGGAGA > >GCCACAGCAACTGTAGATCTCGAAGTTGACAGGGGCAACTAGAGGCCTCAGAATTCT > >CACTCTTGAGGAGAGAAGTCTAAGACCTACAGTATGGTCGGGTTAGTTTTTGTTCCGTC > >GAACCTTGGACTAACCACTGTCTGGATA". > > > >Then I want replace the 2nd long sequence with the 2nd > >short sequence and then repeat this over and over > >again until the last long sequence is reached and > >replaced. I think the only problem is that the > >starting site should not be larger than 193. > >Otherwise, there are > >not enough nucleotides in the long sequence for > >replacement. > > > >Furthurmore, I want to keep track the starting > >replacement site for each long sequence. > > > > > >I am copying my code in the below. > >****************************************** > >use strict; > >use warnings; > > > >my (@short, @long, $offset); # the 'short' array will > >hold the short > > #sequences while 'long' > >array the long sequences > > > >open(FILE1, '<', "short_sequences.txt") || die "Can't > >open short_sequences.txt: $!\n"; > >while(){ > > chomp; > > push(@short, $_); > >} > >close FILE1; #Close the file > > > >open(FILE2, '<', "long_sequences.txt") || die "Can't > >open long_sequences.txt: $!\n"; > >while(){ > > chomp; > > push(@long, $_); > >} > >close FILE2; #Close the file > > > > > ># replacement > >foreach my $short(@short){ > > foreach my $long(@long){ > > $offset = int(rand(length($long)%193)); > > substr($long,$offset,length($short),$short); > > printf "%3d", $offset+1; > > print "\n", $long, "\n"; > > > > } > >} > >******************************************** > > > >But I just realized that there is a problem for the > >two > >loops. The problem is that each short sequence will be > >used to replace all long sequences not the > >corresponding one. > > > >So I seek your suggestions on how to handle two files > >simultaneously for my case. > > > >Thank you very much and look forward to your reply! > > > >Best Regards, > > Alex > > > >__________________________________________________ > >Do You Yahoo!? > >Tired of spam? Yahoo! Mail has the best spam protection around > >http://mail.yahoo.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 > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > From c.klaassen at cwz.nl Fri Jul 22 03:45:11 2005 From: c.klaassen at cwz.nl (=?ISO-8859-1?Q?Corn=E9_HW_Klaassen?=) Date: Fri, 22 Jul 2005 09:45:11 +0200 Subject: [BiO BB] Assemble forward/reverse sequence trace data In-Reply-To: References: Message-ID: <42E0A407.4090401@cwz.nl> Hi All, Can anybody recommend a free software tool (windows compatible) that allows the user to combine forward and reverse sequence trace data into a final assembly? Thanks, Corn? ----------------------------------------------------------------------------------------- dr. Corn? H.W. Klaassen, Molecular Biologist Canisius Wilhelmina Hospital, Molecular Biology Unit, C60-C70 Weg door Jonkerbos 100, 6532 SZ Nijmegen, The Netherlands. tel: #31-24-3658670 (office) tel: #31-24-3658677 (direct) fax: #31-24-3658671 E-Mail: c.klaassen at cwz.nl From ml at mb.au.dk Fri Jul 22 04:04:56 2005 From: ml at mb.au.dk (Martin Luetzelberger) Date: Fri, 22 Jul 2005 10:04:56 +0200 Subject: [BiO BB] Assemble forward/reverse sequence trace data In-Reply-To: <42E0A407.4090401@cwz.nl> References: <42E0A407.4090401@cwz.nl> Message-ID: <6.2.3.4.2.20050722100418.01f52fc0@mail.mb.au.dk> FinchTV might be what you want. http://www.geospiza.com/finchtv/features/index.html At 09:45 AM 7/22/2005, you wrote: >Hi All, > >Can anybody recommend a free software tool >(windows compatible) that allows the user to >combine forward and reverse sequence trace data into a final assembly? > >Thanks, > >Corn? > >----------------------------------------------------------------------------------------- >dr. Corn? H.W. Klaassen, Molecular Biologist >Canisius Wilhelmina Hospital, Molecular Biology Unit, C60-C70 >Weg door Jonkerbos 100, 6532 SZ Nijmegen, The Netherlands. > >tel: #31-24-3658670 (office) >tel: #31-24-3658677 (direct) >fax: #31-24-3658671 >E-Mail: c.klaassen at cwz.nl > >_______________________________________________ >Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From c.klaassen at cwz.nl Fri Jul 22 04:45:28 2005 From: c.klaassen at cwz.nl (=?ISO-8859-1?Q?Corn=E9_HW_Klaassen?=) Date: Fri, 22 Jul 2005 10:45:28 +0200 Subject: [BiO BB] Assemble forward/reverse sequence trace data In-Reply-To: <6.2.3.4.2.20050722100418.01f52fc0@mail.mb.au.dk> References: <42E0A407.4090401@cwz.nl> <6.2.3.4.2.20050722100418.01f52fc0@mail.mb.au.dk> Message-ID: <42E0B228.40003@cwz.nl> Hi Martin, Thanks for this quick reaction, but I'm more looking for a software package that lets me align the forward and reverse traces to produce and export the consensus sequence. I can easily do this with the sequence (text) itself using ClustalX but I would prefer to do this with the sequence traces so that I have a visual check of the bases that have been called. Corn? Martin Luetzelberger wrote: > FinchTV might be what you want. > http://www.geospiza.com/finchtv/features/index.html > > At 09:45 AM 7/22/2005, you wrote: > >> Hi All, >> >> Can anybody recommend a free software tool (windows compatible) that >> allows the user to combine forward and reverse sequence trace data >> into a final assembly? >> >> Thanks, >> >> Corn? >> >> ----------------------------------------------------------------------------------------- >> >> dr. Corn? H.W. Klaassen, Molecular Biologist >> Canisius Wilhelmina Hospital, Molecular Biology Unit, C60-C70 >> Weg door Jonkerbos 100, 6532 SZ Nijmegen, The Netherlands. >> >> tel: #31-24-3658670 (office) >> tel: #31-24-3658677 (direct) >> fax: #31-24-3658671 >> E-Mail: c.klaassen at cwz.nl >> >> _______________________________________________ >> 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 sariego9 at yahoo.com Fri Jul 22 08:19:50 2005 From: sariego9 at yahoo.com (Diego Martinez) Date: Fri, 22 Jul 2005 05:19:50 -0700 (PDT) Subject: [BiO BB] Assemble forward/reverse sequence trace data In-Reply-To: <42E0B228.40003@cwz.nl> Message-ID: <20050722121950.26416.qmail@web32510.mail.mud.yahoo.com> Hello Martin, The classic trace aligner is the Phred-Phrap-Consed package from Phil Green up at UW. it claims it now works on Windows, however, that may mean you have to compile it yourself. I have performed this successfully on Sun, SGI and Linux, but never on Windows. check it out at: http://www.phrap.org/phredphrapconsed.html Diego --- Corn? HW Klaassen wrote: > Hi Martin, > > Thanks for this quick reaction, but I'm more looking for a software > package that lets me align the forward and reverse traces to produce and > export the consensus sequence. I can easily do this with the sequence > (text) itself using ClustalX but I would prefer to do this with the > sequence traces so that I have a visual check of the bases that have > been called. > > Corn? > > Martin Luetzelberger wrote: > > > FinchTV might be what you want. > > http://www.geospiza.com/finchtv/features/index.html > > > > At 09:45 AM 7/22/2005, you wrote: > > > >> Hi All, > >> > >> Can anybody recommend a free software tool (windows compatible) that > >> allows the user to combine forward and reverse sequence trace data > >> into a final assembly? > >> > >> Thanks, > >> > >> Corn? > >> > >> ----------------------------------------------------------------------------------------- > >> > >> dr. Corn? H.W. Klaassen, Molecular Biologist > >> Canisius Wilhelmina Hospital, Molecular Biology Unit, C60-C70 > >> Weg door Jonkerbos 100, 6532 SZ Nijmegen, The Netherlands. > >> > >> tel: #31-24-3658670 (office) > >> tel: #31-24-3658677 (direct) > >> fax: #31-24-3658671 > >> E-Mail: c.klaassen at cwz.nl > >> > >> _______________________________________________ > >> 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 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .=$=. .=$=. .=$=. .=$=. .=$=. .=$=. @ @ | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | @ @ | ~' `~$~' `~$~' `~$~' `~$~' `~$~' `~ ____________________________________________________ Start your day with Yahoo! - make it your home page http://www.yahoo.com/r/hs From ediths at unizh.ch Fri Jul 22 06:03:30 2005 From: ediths at unizh.ch (Edith Schlagenhauf) Date: Fri, 22 Jul 2005 12:03:30 +0200 Subject: [BiO BB] Assemble forward/reverse sequence trace data In-Reply-To: <42E0B228.40003@cwz.nl> References: <42E0A407.4090401@cwz.nl> <6.2.3.4.2.20050722100418.01f52fc0@mail.mb.au.dk> <42E0B228.40003@cwz.nl> Message-ID: Hi Corn?, you may want to have a look at the Staden software at: http://staden.sourceforge.net/ and/or at Phred/Phrap/Consed: http://bozeman.genome.washington.edu/ Another alternative may be Vector NTI which is now FREE for Non-Profit Customers. See at: http://www.invitrogen.com/content.cfm?pageID=10225>http://www.invitrogen.com/content.cfm?pageID=10225 http://www.invitrogen.com/mydetails>http://www.invitrogen.com/mydetails Hope this helps, Edith > > At 09:45 AM 7/22/2005, you wrote: > > > >> Hi All, > >> > >> Can anybody recommend a free software tool (windows compatible) that > >> allows the user to combine forward and reverse sequence trace data > >> into a final assembly? > >> > >> Thanks, > >> > >> Corn? > >> ****************************************** Dr Edith Schlagenhauf Bioinformatics Institute of Plant Biology University of Zurich Zollikerstrasse 107 CH-8008 Zurich SWITZERLAND e-mail: ediths AT botinst DOT unizh DOT ch Tel.: +41 1 634 82 78 Fax : +41 1 634 82 04 ****************************************** From idoerg at burnham.org Fri Jul 22 12:38:40 2005 From: idoerg at burnham.org (Iddo Friedberg) Date: Fri, 22 Jul 2005 09:38:40 -0700 Subject: [BiO BB] Re: pdb-l: Checking homology In-Reply-To: <20050722152416.42487.qmail@web52605.mail.yahoo.com> References: <20050722152416.42487.qmail@web52605.mail.yahoo.com> Message-ID: <42E12110.80708@burnham.org> Anshu, If it is a sequence vs sequence comparison, then you can put the relevant subsequences into bl2seq, or any other pairwise sequence alignment program. http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi If it is sequence vs. structure, i.e. modeling, then you can create a new PDB file by removing all the ATOM records from amino acids not in your subsequence. ./I anshu verma wrote: > Hi, > > I have a protein. A portion of the protein forms a Beta barrel > structure. According to my literature serach, this particular portion > of the protein is analogous to a Beta barrel structure of another > protein whose structure is known. I know BLAST can compare a > particular sequence to the known sequences/ structure in the data > bank. Is there any way of comparing a portion of the sequences of two > proteins? Eg. I want to take a particular portion of* protein A* and > compare it to a *particular portion* of *protein B* whose structure is > known, *but not the entire protein.* > ** > Thanks, > Anshu -- 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 From dmnunif at charter.net Tue Jul 26 12:43:48 2005 From: dmnunif at charter.net (Unifinium Ltd) Date: 26 Jul 2005 16:43:48 GMT Subject: [BiO BB] "Come visit my web site!" Message-ID: This email is being sent to you by the web site notification service at EarthLink. You can see my site here: http://www.plantcarebyunifinium.com/bioinformaticsbyunifiniumltd/ This web site was created with Trellix. Build your own web site at http://www.earthlink.net/biz/hosting From sheehan_rs at yahoo.com Wed Jul 27 15:17:05 2005 From: sheehan_rs at yahoo.com (Richard Sheehan) Date: Wed, 27 Jul 2005 12:17:05 -0700 (PDT) Subject: [BiO BB] Re: "Come visit my web site!" (Unifinium Ltd) In-Reply-To: <20050727160136.31C56D22AC@www.bioinformatics.org> Message-ID: <20050727191706.29558.qmail@web52308.mail.yahoo.com> I visited your web site. I'm sure the content is nice; but I didn't want to waste my time and get eye strain from trying to decipher the text from the mottled background. Try using a different background for the text areas; or better yet, no background at all. You'll probably have a better response for your web site. Just my 2.8 cents. Richard Sheehan > You can see my site here: > http://www.plantcarebyunifinium.com/bioinformaticsbyunifiniumltd/ > > > > > This web site was created with Trellix. Build your > own web site at http://www.earthlink.net/biz/hosting > ____________________________________________________ Start your day with Yahoo! - make it your home page http://www.yahoo.com/r/hs From pjain at xldb.di.fc.ul.pt Thu Jul 28 14:10:30 2005 From: pjain at xldb.di.fc.ul.pt (Pooja Jain) Date: Thu, 28 Jul 2005 19:10:30 +0100 Subject: [BiO BB] Coordinate System for Biomolecules Message-ID: <1122574230.42e91f96455e4@webservices.di.fc.ul.pt> Hi All, Could anybody share the basic concept about different coordinate systems primarily used to describe the 3D structures of DNA, RNA and proteins? Are there any terms like Nucleic Acid Coordinate System and Protein Coordinate System? I was reading basics about Coordinate Systems from Wikipedia but I was unable to correlate it to explain the structure of Biomolecules and to understand how structure simulation/Prediction techniques works using coordinate systems ? Any insight about what I asked or anything related would be greatly appreciated. Thank you. Best Wishes, -Pooja From richard.squires at utsouthwestern.edu Thu Jul 28 15:23:18 2005 From: richard.squires at utsouthwestern.edu (Burke Squires) Date: Thu, 28 Jul 2005 14:23:18 -0500 Subject: [BiO BB] Coordinate System for Biomolecules In-Reply-To: <1122574230.42e91f96455e4@webservices.di.fc.ul.pt> References: <1122574230.42e91f96455e4@webservices.di.fc.ul.pt> Message-ID: Hello Pooja, If I could ask an unrelated questions do you live/work in Portugal? Thanks, Burke Squires -------------------- Burke Squires BioHealthBase Bioinformatic Resource Center UT Southwestern Dallas, Texas richard.squires at utsouthwestern.edu (214) 648-4952 On Jul 28, 2005, at 1:10 PM, Pooja Jain wrote: > Hi All, > > Could anybody share the basic concept about different coordinate > systems > primarily used to describe the 3D structures of DNA, RNA and > proteins? Are > there any terms like Nucleic Acid Coordinate System and Protein > Coordinate > System? > > I was reading basics about Coordinate Systems from Wikipedia but I > was unable > to correlate it to explain the structure of Biomolecules and to > understand > how structure simulation/Prediction techniques works using coordinate > systems ? Any insight about what I asked or anything related would > be greatly > appreciated. > > Thank you. > > Best Wishes, > -Pooja > _______________________________________________ > Bioinformatics.Org general forum - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From daniel.amelang at gmail.com Thu Jul 28 19:05:52 2005 From: daniel.amelang at gmail.com (Daniel Amelang) Date: Thu, 28 Jul 2005 16:05:52 -0700 Subject: [BiO BB] Coordinate System for Biomolecules In-Reply-To: <1122574230.42e91f96455e4@webservices.di.fc.ul.pt> References: <1122574230.42e91f96455e4@webservices.di.fc.ul.pt> Message-ID: Here's a guide about the coordinate system (and file format) that the pdb (protein data bank) uses: http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html Dan From mayagao1999 at yahoo.com Fri Jul 29 20:35:43 2005 From: mayagao1999 at yahoo.com (Alex Zhang) Date: Fri, 29 Jul 2005 17:35:43 -0700 (PDT) Subject: [BiO BB] A problem about a subroutin in my code Message-ID: <20050730003544.95514.qmail@web53503.mail.yahoo.com> Dear all, Sorry to bother you. I need some help on my code. I have an input file named "origin8.txt" which holds 200 short sequences of width 8. My code is to use each short sequence from "origin8.txt" as a template to generate 100 short sequences of the same width and store them in a txt file A. Then the code will read 100 short sequences from the txt file A and 100 long sequences of width 200 from a txt file B , and then replaced a substring of each long sequence using each short sequence. This code will lead to two txt files C and D. File C will hold 100 replaced long sequences. In other words, I want to input "origin8.txt" to get 200 File D. My code can generates 200 File D but each of them holds nothing. So I guess the problem is caused by a failure of passing the data to a subroutine named "make_file". Can anybody suggest me how to modify that? Thank you very much in advance! Sincerely, Alex My code: ******************************************************************* #!/usr/bin/perl use strict; use warnings; my (@origin, $y); my $N_Sequences = 100; my @Alphabet = split(//,'ACGT'); my $P_Consensus = 0.85; # This is the probability of dominant letter # ====== Globals ========================== my @Probabilities; # Stores the probability of each character # ====== Program ========================== open (ORIGIN, "< origin8.txt"); # This file holds 200 sequences used for motif template chomp (@origin = ); close ORIGIN; for ($y=0; $y<=$#origin; $y++) { my @Motif = split(//,'$origin[$y]'); # This is a loop to get the motif template from origin8 open (OUT_NORM, ">short_sequences8_[$y].txt") or die "Unable to open file :$!"; for (my $i=0; $i < $N_Sequences; $i++) { for (my $j=0; $j < scalar(@Motif); $j++) { loadConsensusCharacter($Motif[$j]); addNoiseToDistribution(); convertToIntervals(); print OUT_NORM (getRandomCharacter(rand(1.0))); } print OUT_NORM "\n"; make_files(); } } exit(); # ====== Subroutines ======================= # sub loadConsensusCharacter { my ($char) = @_; my $Found = 'FALSE'; for (my $i=0; $i < scalar(@Alphabet); $i++) { if ( $char eq $Alphabet[$i]) { $Probabilities[$i] = 1.0; $Found = 'TRUE'; } else { $Probabilities[$i] = 0.0; } } if ($Found eq 'FALSE') { die("Panic: Motif-Character\"$char\" was not found in Alphabet. Aborting.\n"); } return(); } # ========================================== sub addNoiseToDistribution { my $P_NonConsensus = ( 1.0-$P_Consensus) / (scalar(@Alphabet) - 1); for (my $i=0; $i < scalar(@Probabilities); $i++) { if ( $Probabilities[$i] == 1.0 ) { $Probabilities[$i] = $P_Consensus; } else { $Probabilities[$i] = $P_NonConsensus; } } return(); } # ========================================== sub convertToIntervals { my $Sum = 0; for (my $i=1; $i < scalar(@Probabilities); $i++) { $Probabilities[$i] += $Probabilities[$i-1]; } return(); } # ========================================== sub getRandomCharacter { my ($RandomNumber) = @_; my $i=0; for ($i=0; $i < scalar(@Probabilities); $i++) { if ($Probabilities[$i] > $RandomNumber) { last; } } return($Alphabet[$i]); } # ========================================== sub make_files { my (@short, @long,$x,$r, $output_norm); open (SHORT, "< short_sequences8_[$y].txt"); chomp (@short = ); close SHORT; open (LONG, "< long_sequences.txt"); chomp (@long = ); close LONG; open (OUT_INITIAL, "> output8_[$y]1.txt"); open (OUT_REPLACED, "> output8_[$y]2.txt"); for ($x=0; $x<=$#short; $x++) { $r=2; print OUT_INITIAL ">SeqName$x\n$long[$x]\n"; print OUT_REPLACED "SeqName$x\n" . substr($long[$x], $r, length $short[$x]) . "\n";} close OUT_INITIAL; close OUT_REPLACED; } ******************************************************************* Input file "origin8.txt" holds 200 sequences as: TTTATAAT TGTCAATG CGTTGATG CGTCCTAG GGCTTCCA ATTAGCCT GTCCTGAT TGTAAATC CGCTTATT TTGACATA CCTGATAT ATGAATCG CGTCCGAT TGGCCCAT ATCCTGAT TGCCCATT CCCTAACT AAAAAAAA TTTTTTTT CCCCCCCC GGGGGGGG AAAAAAAT AAAAAAAG AAAAAAAC AAAAAACC AAAAAATT AAAAAAGG AAAAAACT AAAAAACG AAAAAACA AAAAACAA AAAACAAA AAACAAAA AACAAAAA ACAAAAAA CAAAAAAA AAAAAATA AAAAATAA AAAATAAA AAATAAAA AATAAAAA ATAAAAAA TAAAAAAA AAAAAAGA AAAAAGAA AAAAGAAA AAAGAAAA AAGAAAAA AGAAAAAA GAAAAAAA AAAACCAA AACCAAAA CCAAAAAA AAAATTAA AATTAAAA TTAAAAAA AAAAACCC AAAACCCA AAACCCAA AACCCAAA ACCCAAAA CCCAAAAA AAAAATTT AAAATTTA AAATTTAA AATTTAAA ATTTAAAA TTTAAAAA AAAAAGGG AAAAGGGA AAAGGGAA AAGGGAAA AGGGAAAA GGGAAAAA AAAACCCC AAACCCCA AACCCCAA ACCCCAAA CCCCAAAA AAAATTTT AAATTTTA AATTTTAA ATTTTAAA TTTTAAAA AAAAGGGG AAAGGGGA AAGGGGAA AGGGGAAA GGGGAAAA AAACCCCC AACCCCCA ACCCCCAA CCCCCAAA AAATTTTT AATTTTTA ATTTTTAA TTTTTAAA AAAGGGGG AAGGGGGA AGGGGGAA GGGGGAAA AAGGGGGG AGGGGGGA GGGGGGAA AACCCCCC ACCCCCCA CCCCCCAA AATTTTTT ATTTTTTA TTTTTTAA ATTTTTTT TTTTTTTA ACCCCCCC CCCCCCCA AGGGGGGG GGGGGGGA ATTTTTTT TTTTTTTA ATAAAATA AATAAATA AAATAATA AAAATATA ACAAAACA AACAAACA AAACAACA AAAACACA AGAAAAGA AAGAAAGA AAAGAAGA AAAAGAGA ATAAAAGA ATAAAACA AGAAAATA AGAAAACA ACAAAAGA ACAAAATA ATTAAATA AATTAATA AAATTATA ACCAAACA AACCAACA AAACCACA AGGAAAGA AAGGAAGA AAAGGAGA ATTTAATA AATTTATA ACCCAACA AACCCACA AGGGAAGA AAGGGAGA ATTTAACA ATTTAAGA AATTTACA AATTTAGA ACCCAATA ACCCAAGA AACCCATA AACCCAGA AGGGAACA AGGGAATA AAGGGATA AAGGGACA TTGGGACA CCGGGACA AGAAGGGA TGCCCATA TAAAAAAT TGCCTATA CCGTAGTC ACTTGACT CTGATCCC TGTGACTA CCTGATCC CCTGAACC TGATCACG GGGTAACC CTTTTGAA TTGTATGA CCTGATAA CTGGTTAG CCCCGACC TTGGGGAC GGTTTGAC GCTTAGAC GTTACACC TTGTACCA TGGTACCA CCGTACAT CCCTTGCC GTGTTGGT ATCGATCG ACGTACGT TCAGTCAG GCTATACG GTCCATAC CCGTCCGT ATATATCC GTGTCCCC --------------------------------- Yahoo! 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