From asidhu at biomap.org Mon Jan 1 12:57:59 2007 From: asidhu at biomap.org (Amandeep S. Sidhu) Date: Tue, 2 Jan 2007 04:57:59 +1100 Subject: [BiO BB] CFP: 2nd Ontologies for Biomedical Systems Track with IEEE CBMS 2007 Message-ID: <1167674279.45994ba7080ff@mail.opentransfer.com> 2nd Special Track on Ontologies for Biomedical Systems for 20th IEEE International Symposium on Computer-Based Medical Systems http://cbms07.biomap.org/ Biomedical Ontologies have developed in an uncoordinated way, often reflecting mere relations of 'association' between what are called 'concepts', and serving primarily the purposes of information extraction from on-line biomedical literature and databases. In this track we will broadly cover current research on development biomedical ontologies, and various issues in biomedical informatics addressed by these ontologies. Track will consist of papers in a biomedical informatics sub discipline, refereed by international program committee. Papers selected for this special track should report on significant unpublished work suitable for publication as a conference paper. This track will broadly address following areas: * Conceptual Models for Biological and Medical Data * Biomedical Data Integration, Analysis and Interoperability * Support of Ontologies for Biological Information Retrieval and Web Services * Tools for Development and Management of Biomedical Ontologies Last year the special track on ONTOLOGIES FOR BIOMEDICAL SYSTEMS at CBMS 2006 got a good response and some high quality papers. We have accepted 8 of 17 papers submitted to the track. More information about this track can be found at: http://cbms06.biomap.org/ In recent years, we have learned a great deal about the criteria which must be satisfied if ontology is to allow true information integration and automatic reasoning across data and information derived from different sources. The goal of this track is to survey existing biomedical ontologies and reform them in such a way as to allow true information integration in biomedical domain. Authors are invited to submit original papers exploring the theories, techniques, and applications of biomedical ontologies. Papers are invited (but not limited) to the following themes: * Biomedical Ontologies for Genetics, Proteomics, Diseases, Privacy etc. * Conceptual Models for Biological and Medical Data * Semantics in Biological Data Modeling * Use of semantics to manage Interoperation in Biomedical Databases * Semantic Web technologies and formalisms for Biomedical Data * Ontology representation and exchange languages for bioinformatics * Biomedical Ontologies and OWL * Biological Data Integration and Management using Ontologies * Biomedical Data Engineering using Ontologies * Application of Biomedical Ontologies for Heterogeneous Database Access * Query Optimization Techniques for Biomedical Database using Ontologies * Support of Ontologies for Biological Information Retrieval and Web Services * Change Management in Biomedical Ontologies * Tools for Development and Management of Biomedical Ontologies Special Issue and Edited Book For second year, we will be running a Special Issue of International Journal of Bioinformatics Research and Applications (IJBRA) on "Ontologies for Bioinformatics II" in early 2008. Current issue of Ontologies for Bioinformatics, to be published in 2007 received 24 papers of which 8 are accepted. High Quality submissions will be published as book chapters in book entitled "Biomedical Data and Applications", as a part of Series of Studies in Computational Intelligence of Springer in late 2007. Important Dates January 31, 2007 Submission of a 3-page paper summary March 15, 2007 Notification of acceptance April 15, 2007 Final camera-ready paper (6 pages, maximum) due April 15, 2007 Pre-registration deadline Paper Submission and Publication Submitted papers have to be original, containing new and original results. There are two possibilities for initially submitting a paper: * A full paper (6 pages). It is strongly encouraged to submit a full paper, which enables reviewers to assess it more objectively and authors to substantially improve the paper based on the review feedback. In this way, the high quality of this conference series can be adequately maintained and/or improved. * A summary (3 pages). CBMS 2007 serves also as a forum for exchanging interesting and novel results of a work in progress and in this manner provides participants with an opportunity to come up-to-date on important issues. In this way, the 3-pages summaries are also accepted in the case that a full paper can not be delivered until the deadline. There are two possibilities for presenting an accepted paper: oral presentation (regular papers) or poster presentation (short papers). Authors can also indicate their preference when submitting a paper. The final decision will be made by the Program Committee based on the reviews. All papers will be peer-reviewed by at least two reviewers. Submission implies the willingness of at least one of the authors to register and present the paper at the CBMS 2007 Symposium. All papers will be peer reviewed by at least two independent referees. All accepted papers will be included in the conference proceedings. Additionally, selected high quality papers may be invited to submit a substantially extended version for the special issue of an international medical informatics journal (Journal of Medical Systems, International Journal of Medical Informatics, IEEE Transactions on Information Technology in Biomedicine,Computer methods and programs in biomedicine). At least one of authors must pre-register to have the paper published in the proceedings. If you only plan to attend and are not submitting a paper, pre-registration is still strongly encouraged. This conference is space-limited, and registration may not be available on-site. For further questions, please contact technical program chair: cbms07 at biomap.org Track Chairs * Tharam S. Dillon (University of Technology Sydney, Australia) * Elizabeth Chang (Curtin University of Technology, Australia) Technical Program Chairs * Amandeep S. Sidhu (University of Technology Sydney, Australia) * Jake Chen (Indiana University, USA) Track Program Committee Alexey Tsymbal (Siemens, Germany) David Hansen (e-Health Research Centre, CSIRO, Australia) David Taniar (Monash University, Australia) Ernesto Damiani (Computer Science Department, Milan University, Italy) Fabio Porto (Database Laboratory, EPFL, Switzerland) Farookh K. Hussain (Curtin University of Technology, Australia) Fedja Hadzic (University of Technology Sydney, Australia) Jake Chen (Indiana University, USA) Jason Wang (New Jersey Institute of Technology, USA) Li Liao (University of Delaware, USA) Ling Feng (Tsinghua University, China) Maja Hadzic (Curtin University of Technology, Australia) Mustafa Jarrar (Vrije Universiteit Brussel, Belgium) Pornpit Wongthongtham (Curtin University of Technology, Australia) Rajugan Rajagopalapillai (University of Technology Sydney, Australia) Robert Meersman (Vrije Universiteit Brussel, Belgium) Silke Eckstein (Technical University of Braunschweig, Germany) Sourav S Bhowmick (Nanyang Technological University, Singapore) Sun Kim (School of Informatics, Indiana University, USA) Vicky Nassis (La Trobe University, Australia) Wenny Rahayu (La Trobe University, Australia) -- Amandeep S. Sidhu, MIEEE, MACM, MACS, MISCB Senior Researcher (Bioinformatics) Room CB10.04.130 Faculty of Information Technology University of Technology, Sydney PO Box 123 Broadway, NSW 2007, Australia UTS Email: asidhu"AT SIGN"it.uts.edu.au Personal Email: asidhu"AT SIGN"biomap.org Personal Web: http://www.amandeep.org/ Project Web: http://www.proteinontology.info/ Ph: +61 2 9514 4469 Fax: +61 2 9514 1807 Mobile: +61 448897900 From sswang at berkeley.edu Tue Jan 2 17:37:37 2007 From: sswang at berkeley.edu (Sarah Wang) Date: Tue, 02 Jan 2007 14:37:37 -0800 Subject: [BiO BB] How to make a plot of phylogenetic profile? Message-ID: Hi, Can anybody give me a hint of how to do this: I want to make a plot -- heat map like but without color gradient for phylogenetic profile. I've seen these plots in publications but don't know how to make one. What I want is for example, the columns are 100 genes (orthologs, only one best hit for one species), the rows are 100 species, if an ortholog exist in for a gene in a species, the corresponding cell is shaded. I use R and Perl but not Matlab. Thanks From landman at scalableinformatics.com Tue Jan 2 23:56:19 2007 From: landman at scalableinformatics.com (Joe Landman) Date: Tue, 02 Jan 2007 23:56:19 -0500 Subject: [BiO BB] Announcing MPI-HMMer Message-ID: <459B3773.1090104@scalableinformatics.com> Hi folks: Short OT break. http://code.google.com/p/mpihmmer/ an MPI implementation of HMMer 2.3.2. More details soon at bioinformatics.org and other places. RPMs from http://downloads.scalableinformatics.com/downloads/mpihmmer Back to your regularly scheduled cluster/informatics. Joe -- Joseph Landman, Ph.D Founder and CEO Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://www.scalableinformatics.com phone: +1 734 786 8423 fax : +1 734 786 8452 or +1 866 888 3112 cell : +1 734 612 4615 From leo at corn.ab.a.u-tokyo.ac.jp Wed Jan 3 10:45:55 2007 From: leo at corn.ab.a.u-tokyo.ac.jp (Leonardo Martins) Date: Thu, 4 Jan 2007 00:45:55 +0900 Subject: [BiO BB] How to make a plot of phylogenetic profile? In-Reply-To: References: Message-ID: <20070103154555.GA13514@lbm.ab.a.u-tokyo.ac.jp> As spoken by Sarah Wang: > Hi, > > Can anybody give me a hint of how to do this: > I want to make a plot -- heat map like but without color gradient for > phylogenetic profile. I've seen these plots in publications but don't know > how to make one. > What I want is for example, the columns are 100 genes (orthologs, only one > best hit for one species), the rows are 100 species, if an ortholog exist in > for a gene in a species, the corresponding cell is shaded. > I use R and Perl but not Matlab. I believe that, in R, the function "heatmap()" will do the trick. If your data is a matrix with 0's and 1's, then you can try > heatmap (mydata, col=c("white","black"), scale="none") (where the option "scale" is redundant, but will prevent the normal standardization of the rows). If you don't need the dendrogram produced, just add the options "Colv=NA" and "Rowv=NA". Or you may use the underlying "image()" function. Sincerely, Leo -- -- Leonardo de Oliveira Martins Mobile: 080-3395-6334 ???????????????? ???????? Biometrics Laboratory at the University of Tokyo, Japan ---------------------------------------------------------- From skhadar at gmail.com Thu Jan 4 11:12:17 2007 From: skhadar at gmail.com (Shameer Khadar) Date: Thu, 4 Jan 2007 08:12:17 -0800 Subject: [BiO BB] Modeling of small peptides Message-ID: Dear All, What is the best approach to model small peptides ? Is it homology (i think ... no ! ) or ab-initio or any other efficient methods or servers / programs available ? Please share your knowledge, Thanks in advance !!! -- S K From kiran.soorya at gmail.com Thu Jan 4 01:58:31 2007 From: kiran.soorya at gmail.com (soorya kiran) Date: Thu, 4 Jan 2007 12:28:31 +0530 Subject: [BiO BB] Are there servers or programs Message-ID: Are there servers or programs (which are downloadable) which can used for structure alignment of proteins and where we can get the atomic co-ordinates of the protein after alignment? Srijith, SooryaKiran Bioinformatics (P) LTD, Industry Incubation Centre, University of Kerala, Karyavattom Campus, Thiruvananthapuram, Keralam, India. 695 581 Ph : +91 (471) 2414593 www.sooryakiran.com Email : kiran.soorya at gmail.com Confidentiality Statement :- The contents of this e-mail, including its attachment, are intended for the exclusive use of the recipient and may contain confidential or privileged information. If you are not the intended recipient, you are strictly prohibited from reading, using, disclosing, copying, or distributing this e-mail or any of its contents. If you received this e-mail in error, please notify the sender by reply e-mail immediately and permanently delete this e-mail and its attachments, along with any copies thereof. Thank you. -- From lixue at iastate.edu Thu Jan 4 13:37:04 2007 From: lixue at iastate.edu (Xue, Li) Date: Thu, 4 Jan 2007 12:37:04 -0600 (CST) Subject: [BiO BB] Modeling of small peptides Message-ID: <4371240107430@webmail.iastate.edu> As far as I know, both Hidden Markov Model and SVM have been used in modeling small peptides. Li > Dear All, > > What is the best approach to model small peptides ? > Is it homology (i think ... no ! ) or ab-initio or any other efficient > methods or servers / programs available ? > > Please share your knowledge, > Thanks in advance !!! > -- > S K > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Xue, Li Bioinformatics and Computational Biology Iowa State University, Ames, IA 50011 515-520-1676 From raghu at velgonda.cs.qc.cuny.edu Thu Jan 4 13:17:57 2007 From: raghu at velgonda.cs.qc.cuny.edu (Raghu Prasad Rao, METPALLY) Date: Thu, 4 Jan 2007 13:17:57 -0500 (EST) Subject: [BiO BB] Modeling of small peptides In-Reply-To: <20070104170130.4FA403685F6@primary.bioinformatics.org> Message-ID: hi shameer, If you know the homologous peptide fragment with known structure corresponding your target peptide then using SCWRL program you can replace side chains and minimize it to get fairly good initial model. SCWRL is available form Dunbracks lab http://dunbrack.fccc.edu/SCWRL3.php Web Server: http://www1.jcsg.org/scripts/prod/scwrl/serve.cgi or you can also use one of the modules of SYBYL or insightII to model small peptides. or use The Dundee PRODRG2 Server http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ or use DSDBASE to model disulphide rich peptides http://caps.ncbs.res.in/dsdbase/dsdbase.html all the above and many more softwares are available with different rates of accuracies. cheers raghu > Dear All, > > What is the best approach to model small peptides ? > Is it homology (i think ... no ! ) or ab-initio or any other efficient > methods or servers / programs available ? > > Please share your knowledge, > Thanks in advance !!! > -- > S K > > > ------------------------------ > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > End of BiO_Bulletin_Board Digest, Vol 27, Issue 4 > ************************************************* > From ykalidas at gmail.com Thu Jan 4 22:22:17 2007 From: ykalidas at gmail.com (Kalidas Yeturu) Date: Fri, 5 Jan 2007 08:52:17 +0530 Subject: [BiO BB] Are there servers or programs In-Reply-To: References: Message-ID: <5632703b0701041922t5952f841o211fd567b510ba4@mail.gmail.com> Hi you may get the open-source software for structural alignment: ftp://ftp.sdsc.edu/pub/sdsc/biology/CE/src/ regards kalidas. y On 1/4/07, soorya kiran wrote: > > Are there servers or programs (which are downloadable) which can used > for structure alignment of proteins and where we can get the atomic > co-ordinates of the protein after alignment? > > > Srijith, > SooryaKiran Bioinformatics (P) LTD, > Industry Incubation Centre, > University of Kerala, > Karyavattom Campus, > Thiruvananthapuram, > Keralam, > India. 695 581 > Ph : +91 (471) 2414593 > www.sooryakiran.com > Email : kiran.soorya at gmail.com > > > Confidentiality Statement :- The contents of this e-mail, including its > attachment, are intended for the exclusive use of the recipient and may > contain confidential or privileged information. If you are not the > intended > recipient, you are strictly prohibited from reading, using, disclosing, > copying, or distributing this e-mail or any of its contents. If you > received this e-mail in error, please notify the sender by reply e-mail > immediately and permanently delete this e-mail and its attachments, along > with any copies thereof. Thank you. > > -- > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Kalidas Y http://ssl.serc.iisc.ernet.in/~kalidas From skhadar at gmail.com Fri Jan 5 00:36:52 2007 From: skhadar at gmail.com (Shameer Khadar) Date: Fri, 5 Jan 2007 11:06:52 +0530 Subject: [BiO BB] Are there servers or programs In-Reply-To: References: Message-ID: Hi, There are plenty of programs/webservers available for structure alignment. First of all try this Wiki : http://en.wikipedia.org/wiki/Structural_alignment_software . It is a good starting point. Your second requirement is not clear to me May be PASS2 Database @ NCBS : http://caps.ncbs.res.in/pass2 or DALI at EBIwill be useful to you. Thanks, Shameer On 1/4/07, soorya kiran wrote: > > Are there servers or programs (which are downloadable) which can used > for structure alignment of proteins and where we can get the atomic > co-ordinates of the protein after alignment? > > > Srijith, > SooryaKiran Bioinformatics (P) LTD, > Industry Incubation Centre, > University of Kerala, > Karyavattom Campus, > Thiruvananthapuram, > Keralam, > India. 695 581 > Ph : +91 (471) 2414593 > www.sooryakiran.com > Email : kiran.soorya at gmail.com > > > Confidentiality Statement :- The contents of this e-mail, including its > attachment, are intended for the exclusive use of the recipient and may > contain confidential or privileged information. If you are not the > intended > recipient, you are strictly prohibited from reading, using, disclosing, > copying, or distributing this e-mail or any of its contents. If you > received this e-mail in error, please notify the sender by reply e-mail > immediately and permanently delete this e-mail and its attachments, along > with any copies thereof. Thank you. > > -- > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From skhadar at gmail.com Fri Jan 5 00:55:24 2007 From: skhadar at gmail.com (Shameer Khadar) Date: Fri, 5 Jan 2007 11:25:24 +0530 Subject: [BiO BB] Modeling of small peptides In-Reply-To: <4371240107430@webmail.iastate.edu> References: <4371240107430@webmail.iastate.edu> Message-ID: Dear Li, Thanks for your reply. It will be great if you can point me towards any lierature / web reference. Thanks, Shameer On 1/5/07, Xue, Li wrote: > > As far as I know, both Hidden Markov Model and SVM have been used in > modeling > small peptides. > > Li > > Dear All, > > > > What is the best approach to model small peptides ? > > Is it homology (i think ... no ! ) or ab-initio or any other efficient > > methods or servers / programs available ? > > > > Please share your knowledge, > > Thanks in advance !!! > > -- > > S K > > _______________________________________________ > > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > Xue, Li > Bioinformatics and Computational Biology > Iowa State University, Ames, IA 50011 > 515-520-1676 > > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From a.gopee at utm.intnet.mu Fri Jan 5 01:36:43 2007 From: a.gopee at utm.intnet.mu (ajit) Date: Fri, 5 Jan 2007 10:36:43 +0400 Subject: [BiO BB] Computational prroaches to protein structure and function prediction Message-ID: <00d101c73094$9c4eee20$150d7bca@Ajit> Hello Can anybody tell me where to get the latest news/articles/published papers on computational approaches to Protein structure and/or protein function prediction? Is there any research group working on this topic? I'm interested in carrying out research in this topic. Thanks Happy new year 2007 to all of you Regards Ajit From skhadar at gmail.com Fri Jan 5 00:39:47 2007 From: skhadar at gmail.com (Shameer Khadar) Date: Fri, 5 Jan 2007 11:09:47 +0530 Subject: [BiO BB] Are there servers or programs In-Reply-To: References: Message-ID: You can also try HOMSTRAD : http://www-cryst.bioc.cam.ac.uk/homstrad/ DALI : http://www.ebi.ac.uk/dali/ On 1/5/07, Shameer Khadar wrote: > > Hi, > There are plenty of programs/webservers available for structure > alignment. First of all try this Wiki : > http://en.wikipedia.org/wiki/Structural_alignment_software . It is a good > starting point. > > Your second requirement is not clear to me > May be PASS2 Database @ NCBS : http://caps.ncbs.res.in/pass2 or DALI at EBIwill be useful to you. > > Thanks, > Shameer > > On 1/4/07, soorya kiran wrote: > > > > Are there servers or programs (which are downloadable) which can used > > for structure alignment of proteins and where we can get the atomic > > co-ordinates of the protein after alignment? > > > > > > Srijith, > > SooryaKiran Bioinformatics (P) LTD, > > Industry Incubation Centre, > > University of Kerala, > > Karyavattom Campus, > > Thiruvananthapuram, > > Keralam, > > India. 695 581 > > Ph : +91 (471) 2414593 > > www.sooryakiran.com > > Email : kiran.soorya at gmail.com > > > > > > Confidentiality Statement :- The contents of this e-mail, including its > > attachment, are intended for the exclusive use of the recipient and may > > contain confidential or privileged information. If you are not the > > intended > > recipient, you are strictly prohibited from reading, using, disclosing, > > copying, or distributing this e-mail or any of its contents. If you > > received this e-mail in error, please notify the sender by reply e-mail > > immediately and permanently delete this e-mail and its attachments, > > along > > with any copies thereof. Thank you. > > > > -- > > _______________________________________________ > > General Forum at Bioinformatics.Org - > > BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > From uma_25984 at yahoo.co.in Fri Jan 5 02:51:50 2007 From: uma_25984 at yahoo.co.in (umaa) Date: Fri, 5 Jan 2007 13:21:50 +0530 (IST) Subject: [BiO BB] Computational prroaches to protein structure and function prediction Message-ID: <20070105075150.92621.qmail@web8703.mail.in.yahoo.com> Hiiiiiii..... subscribe urself to biomedcentral.com at bioinformatics link... then you can come across the recent articles and latest news -------uma ----- Original Message ---- From: ajit To: The general forum at Bioinformatics.Org Sent: Friday, 5 January, 2007 12:06:43 PM Subject: [BiO BB] Computational prroaches to protein structure and function prediction Hello Can anybody tell me where to get the latest news/articles/published papers on computational approaches to Protein structure and/or protein function prediction? Is there any research group working on this topic? I'm interested in carrying out research in this topic. Thanks Happy new year 2007 to all of you Regards Ajit _______________________________________________ General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board __________________________________________________________ Yahoo! India Answers: Share what you know. Learn something new http://in.answers.yahoo.com/ From lixue at iastate.edu Fri Jan 5 10:53:35 2007 From: lixue at iastate.edu (Xue, Li) Date: Fri, 5 Jan 2007 09:53:35 -0600 (CST) Subject: [BiO BB] Modeling of small peptides Message-ID: <3553950107540@webmail.iastate.edu> Hi Shameer, Here are some links: 1. HMM method for prediction of signal peptides: http://www.cbs.dtu.dk/services/SignalP/abstract.php 2. Support Vector Machine Prediction Of Signal Peptide Cleavage Site (2002) http://citeseer.ist.psu.edu/526978.html Both SVM and HMM are Data Mining approach. Hope this will help. Li > Dear Li, Thanks for your reply. > It will be great if you can point me towards any lierature / web reference. > Thanks, > Shameer > > On 1/5/07, Xue, Li wrote: > > > > As far as I know, both Hidden Markov Model and SVM have been used in > > modeling > > small peptides. > > > > Li > > > Dear All, > > > > > > What is the best approach to model small peptides ? > > > Is it homology (i think ... no ! ) or ab-initio or any other efficient > > > methods or servers / programs available ? > > > > > > Please share your knowledge, > > > Thanks in advance !!! > > > -- > > > S K > > > _______________________________________________ > > > General Forum at Bioinformatics.Org - > > BiO_Bulletin_Board at bioinformatics.org > > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > > > > Xue, Li > > Bioinformatics and Computational Biology > > Iowa State University, Ames, IA 50011 > > 515-520-1676 > > > > > > > > _______________________________________________ > > General Forum at Bioinformatics.Org - > > BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Xue, Li Bioinformatics and Computational Biology Iowa State University, Ames, IA 50011 515-520-1676 From aloraine at gmail.com Fri Jan 5 18:36:09 2007 From: aloraine at gmail.com (Ann Loraine) Date: Fri, 5 Jan 2007 17:36:09 -0600 Subject: [BiO BB] probe behavior - papers? Message-ID: <83722dde0701051536w32dade38kdf64ed4912199327@mail.gmail.com> Hello all, I'm looking for articles or research anyone might have done into the long-range behavior of individual probes on olignucleotide arrays, esp. Affymetrix arrays. I hoping to find an example of how some-one has used a large storehouse of microarray data (e.g., CEL files or probe intensity values) to investigate how different probes perform in lots of different settings and samples. I need this as background research for an array design project :-) Yours, Ann -- Ann Loraine Assistant Professor Departments of Genetics, Biostatistics University of Alabama at Birmingham http://www.transvar.org From marchywka at hotmail.com Fri Jan 5 16:27:49 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Fri, 05 Jan 2007 16:27:49 -0500 Subject: [BiO BB] Are there servers or programs In-Reply-To: Message-ID: I can verify that this link http://biotool.uni-koeln.de:8080/3dalign_neu/cgi-bin/3daligner.py ( liinked from http://www.cgl.ucsf.edu/home/meng/grpmt/structalign.html) did function. I was able to compare two pdb files ( my current thing is oxidized cysteines so I compared: http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?form=6&db=t&Dopt=s&uid=23527 to http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?form=6&db=t&Dopt=s&uid=23526 ) I downloaded the result and it even displayed in the rasmol I built under cygwin. The resulting composite file was reasonably easy to manipulate- I can find the modified sulfur and see how much it moved. I'm not sure what original poster meant about returning coordinants but they should be pretty easy to extract. I think most of the stuff that came up displayed in rasmol or jmol. FWIW, I got this to build but it doesn't seem to generate any output: ftp://ftp.sdsc.edu/pub/sdsc/biology/CE/src/ ( note new address as of 10-06) Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165r ( NOTE MORE NEWER NUMBER ) 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only >From: "Shameer Khadar" >Reply-To: "General Forum at Bioinformatics.Org" > >To: "General Forum at Bioinformatics.Org" > >Subject: Re: [BiO BB] Are there servers or programs >Date: Fri, 5 Jan 2007 11:09:47 +0530 > >You can also try >HOMSTRAD : http://www-cryst.bioc.cam.ac.uk/homstrad/ >DALI : http://www.ebi.ac.uk/dali/ > >On 1/5/07, Shameer Khadar wrote: >> >>Hi, >>There are plenty of programs/webservers available for structure >>alignment. First of all try this Wiki : >>http://en.wikipedia.org/wiki/Structural_alignment_software . It is a good >>starting point. >> >>Your second requirement is not clear to me >>May be PASS2 Database @ NCBS : http://caps.ncbs.res.in/pass2 or >>DALI at EBIwill be useful to you. >> >>Thanks, >>Shameer >> >>On 1/4/07, soorya kiran wrote: >> > >> > Are there servers or programs (which are downloadable) which can used >> > for structure alignment of proteins and where we can get the atomic >> > co-ordinates of the protein after alignment? >> > >> > >> > Srijith, >> > SooryaKiran Bioinformatics (P) LTD, >> > Industry Incubation Centre, >> > University of Kerala, >> > Karyavattom Campus, >> > Thiruvananthapuram, >> > Keralam, >> > India. 695 581 >> > Ph : +91 (471) 2414593 >> > www.sooryakiran.com >> > Email : kiran.soorya at gmail.com >> > >> > >> > Confidentiality Statement :- The contents of this e-mail, including its >> > attachment, are intended for the exclusive use of the recipient and may >> > contain confidential or privileged information. If you are not the >> > intended >> > recipient, you are strictly prohibited from reading, using, disclosing, >> > copying, or distributing this e-mail or any of its contents. If you >> > received this e-mail in error, please notify the sender by reply e-mail >> > immediately and permanently delete this e-mail and its attachments, >> > along >> > with any copies thereof. Thank you. >> > >> > -- >> > _______________________________________________ >> > General Forum at Bioinformatics.Org - >> > BiO_Bulletin_Board at bioinformatics.org >> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> > >> >> >_______________________________________________ >General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ Get live scores and news about your team: Add the Live.com Football Page www.live.com/?addtemplate=football&icid=T001MSN30A0701 From nadia.bolshakova at gmail.com Tue Jan 9 14:43:31 2007 From: nadia.bolshakova at gmail.com (Nadia Bolshakova) Date: Tue, 9 Jan 2007 19:43:31 -0000 Subject: [BiO BB] Call for Special Track "BIOINFORMATICS and its MEDICAL APPLICATIONS" papers Message-ID: <002d01c73426$73b96540$6401a8c0@HUM> 20th IEEE International Symposium on COMPUTER-BASED MEDICAL SYSTEMS (IEEE CBMS 2007) Maribor, Slovenia June 20-22, 2007 Special Track: BIOINFORMATICS and its MEDICAL APPLICATIONS http://www.cs.tcd.ie/~zamolota/CBMS_Bioinformatics07.html CALL FOR PAPERS Major computational challenges have been raised in the post-genomic era. Novel computational methods and approaches are required to acquire, store, organize, archive, analyse and visualize the large amount of biological and biomedical data. The goal of the track is to share ideas related to bioinformatics challenge among biological, biomedical and computer scientists. Authors are invited to submit original papers addressing any computational biology issue. Papers are invited (but not limited) to the following key themes: Biomedical Research Evolution and Phylogenetics Data Mining in Bioinformatics Microarray Analysis RNAi Analysis Sequence Alignment Pathways, Networks, Systems Biology Functional Genomics Visualization Protein Structure and Analysis Comparative Genomics Pattern Recognition Ontologies Software Systems IMPORTANT DATES January 31, 2007 Deadline for paper submissions March 15, 2007 Notification of acceptance April 15, 2007 Final camera-ready paper (6 pages, maximum) due April 15, 2007 Pre-registration deadline SUBMISSION PROCEDURES FOR PAPER No hardcopy submissions are being accepted. Electronic submissions of original technical research papers will only be accepted in PDF format. File size is limited to 2 MB. Use a maximum of six A4 pages, including figures and references. Include one cover sheet, stating the track title (Special Track on Bioinformatics and its Medical Applications), paper title, authors, technical area(s) covered in the article, corresponding author's information (telephone, fax, mailing address, e-mail address), and your preference for oral or poster presentation. Author names should appear only on the cover sheet, not on the paper. Submit your manuscript no later than January 31, 2007. Authors will be notified of acceptance by March 15, 2007 after a review process by three independent experts. Each accepted paper to the Special Track on Bioinformatics and its Medical Applications will be published in the conference proceedings by IEEE CS Press, conditional upon the author's advance registration. Papers that were not accepted by the Program Committee of the track can be considered for publication as regular submissions by the General Program Committee of IEEE CBMS 2007. For more details please see the website of IEEE CBMS 2006: (http://cbms2007.uni-mb.si/?id=6). TRACK PROGRAM COMMITTEE Aedin Culhane Dana-Farber Cancer Institute, USA Fernando Martin-Sanchez Institute of Health "Carlos III", Spain James McInerney National University of Ireland Heather Ruskin Dublin City University, Ireland Anton Zamolotskikh Trinity College Dublin, Ireland Huiru Zheng University of Ulster, Northern Ireland From valenti at dsi.unimi.it Fri Jan 12 05:24:31 2007 From: valenti at dsi.unimi.it (Giorgio Valentini) Date: Fri, 12 Jan 2007 11:24:31 +0100 Subject: [BiO BB] CIBB 2007: second CFP Message-ID: <45A761DF.2060905@dsi.unimi.it> Apologizes for cross-posting. ************************** SECOND CALL FOR PAPERS ************************** CIBB 2007 - Fourth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics Hotel Portofino Kulm - Portofino Vetta, Ruta di Camogli (Genova), Italy July 7-10, 2007 Conference website: http://cibb07.dsi.unimi.it The main goal of this meeting is to provide a forum open to researchers from different disciplines to present and discuss problems relative to computational techniques in bioinformatics with a particular focus on supervised and unsupervised machine learning methods. Topics of interest include, but are not limited to: sequence analysis; transcriptomics; proteomics; evolution and philogeny; comparative genomics; bio-medical text mining and imaging; heterogeneous data integration for diagnostics. For a more detailed list of covered research areas, please visit our website: http://cibb07.dsi.unimi.it. We invite to submit papers that will be published on Springer's Lecture Notes on Computer Science. Selected papers will be invited to submit an extended version to a special issue of Artificial Intelligence in Medicine. The scientific program will include, besides an invited talk of Joaquin Dopazo (Centro de Investigaci?n Pr?ncipe Felipe, Valencia, Spain), accepted papers that will be presented in plenary oral sessions. ********************* Paper submission: ********************* Papers must be written in Latex in Lecture Notes on Computer Science Springer format following the guidelines for "Proceedings and Other Multi-author Volumes (http://www.springer.com). Latex templates can be downloaded from the Springer website or from the conference website. Papers must be no longer than 6 pages, with an additional cover sheet stating paper title, keyword(s), authors names and affiliations, contact author's name and contact details including telephone/fax numbers and e-mail address, and an abstract no more than 200 words long. Papers in pdf format should be sent in attachment by e-mail to infocibb07 at dsi.unimi.it. All accepted papers submitted by registered participants to CIBB 2007 will be published in the Lecture Notes on Computer Science Series, Springer. Selected papers will be invited to submit an extended version for a special issue of Artificial Intelligence in Medicine on "Computational Intelligence methods for Bioinformatics and Biostatistics". CIBB 2007 is jointly organized by - INNS, International Neural Network Society, SIG Bioinformatics - BITS, Bioinformatics ITalian Society - SIREN, Italian Society of Neural Networks - DSI, Dipartimento di Scienze dell'Informazione, Unversit? degli Studi di Milano. - DMI, Dipartimento di Matematica e Informatica, Universit? di Salerno and in connection with WILF 2007 (http://wilf2007.disi.unige.it). ********************* Important Dates: ********************* Submission deadline: January 31 2007 Notification of acceptance: February 28 2007 Final papers due: March 31 2007 Workshop: 7-10 July 2007. ********************* Organizers: ********************* Roberto Tagliaferri, Universit? di Salerno, Italy Giorgio Valentini, Universit? degli Studi di Milano, Italy ****************************************** Scientific Program Committee: ****************************************** Klaus-Peter Adlassnig, Medical University of Vienna, Austria Pierre Baldi, University of California, Irvine, USA Alberto Bertoni, Universit? degli Studi di Milano, Italy Paola Campadelli, Universit? degli Studi di Milano, Italy Nello Cristianini, University of Bristol, UK Giovanni Cuda, Universit? di Catanzaro, Italy Diego di Bernardo, Telethon Institute of Genetics and Medicine, Italy Joaquin Dopazo, Centro de Investigaci?n Pr?ncipe Felipe, Valencia, Spain Sandrine Dudoit, University of California, Berkeley, USA Jon Garibaldi, University of Nottingham, UK Emmanuel Ifeachor, University of Plymouth, UK Nathan Intrator, Tel Aviv University, Israel Nik Kasabov, Auckland University of Technology, NZ Samuel Kaski, Helsinki University of Technology, Finland Natalio Krasnogor, University of Nottingham, UK Luciano Milanesi, ITB CNR, Italy Sushmita Mitra, Indian Statistical Institute, Kolkata, India Marco Muselli, CNR Genova, Italy Oleg Okun, University of Oulu, Finland Alberto Paccanaro,Yale University, CT, USA Giulio Pavesi, Universit? degli Studi di Milano, Italy David Alejandro Pelta, University of Granada, Spain Graziano Pesole, Universit? di Bari, Italy Leif E. Peterson, Baylor College of Medicine Houston, TX, USA Volker Roth, ETH Zurich, Switzerland Udo Seiffert, Leibniz Institute, Gatersleben, Germany Anna Tramontano, Universit? di Roma "La Sapienza", Italy Jean Philippe Vert, Centre for Computational Biology Ecole des Mines de Paris, France *************************************************************** We are looking forward to meet you in Portofino! Roberto Tagliaferri and Giorgio Valentini -- =========================================== Giorgio Valentini D.S.I. - Universita' degli Studi di Milano - Italia Phone: +39 (02) 503.16225 e-mail: valentini at dsi.unimi.it http://homes.dsi.unimi.it/~valenti =========================================== From paakhan at gmail.com Sat Jan 13 00:36:42 2007 From: paakhan at gmail.com (pathan khan) Date: Sat, 13 Jan 2007 11:06:42 +0530 Subject: [BiO BB] Hello need info Message-ID: Hello I have generated a few ESTs from my experiments and have some questions to be addressed...I will be very happy to get suggestions and Help in this regard.. 1. do contigs similar in base composition correspond to the same gene? if not what could be the possible explanation? 2.Why are my ESTs not showing Hits with the already deposited ESTs of the same organism although the protein for which they are coding are identical but from different organisms. Waiting for suggestions Regards Akbar From timmcilveen at talktalk.net Sun Jan 14 19:07:02 2007 From: timmcilveen at talktalk.net (tim) Date: Mon, 15 Jan 2007 00:07:02 +0000 Subject: [BiO BB] Python or Perl Message-ID: <45AAC5A6.7040704@talktalk.net> Hi, I am a final year Molecular Sciences student (chemistry and molecular biology) and am trying to teach myself some bioinformatics programming. My history is in Basic from years ago. Because of this, I find Python a bit easier to understand. Having said this, is biopython widely used, or would I be as well persevering with learning Perl, and then bioperl which seems to have a bigger following? Just one more question. Are most people involved in bioinformatics programming working in industry/academia , are are there people involved in open access , internet based projects? - just curious! Tim From christoph.gille at charite.de Mon Jan 15 02:37:09 2007 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Mon, 15 Jan 2007 08:37:09 +0100 (CET) Subject: [BiO BB] Python or Perl In-Reply-To: <45AAC5A6.7040704@talktalk.net> References: <45AAC5A6.7040704@talktalk.net> Message-ID: <43070.141.42.56.114.1168846629.squirrel@webmail.charite.de> It is really a question of taste what language to chose. It also depends on whether you want to do text processing or number crunching or 3D-visualization or Web-programming. Also look at the respective www.xBio.org libraries whether they contain the methods you need. Number crunching in Python and Perl is slow whereas the string libraries in Python and Perl are very fast. Both are about 10x faster than PHP. Number crunching in Java is as fast (about as fast as C++) and has the advantage that many errors already show up at compile time and not only at runtime which is good for large projects. String processing in Java however is slow. Python and Perl have more elegant syntax and you programs are much shorter. From marchywka at hotmail.com Mon Jan 15 09:25:02 2007 From: marchywka at hotmail.com (Mike Marchywka) Date: Mon, 15 Jan 2007 09:25:02 -0500 Subject: [BiO BB] Python or Perl In-Reply-To: <45AAC5A6.7040704@talktalk.net> Message-ID: Without knowing any important details ( see questions below), if you want to learn more modern programming beyond a few bio packages, I would exapnd on the other reply to your post and would recommend downloading cygwin ( cygwin.com and associated mail lists ) and java from sun. The Sun tutorials should be good OO intros, the Java runtime gives you getter diagnostics for learning- I wouldn't jump from interpretted runtime to C+ right away and the scripting, while important and powerful, doesn't always produce helpful error messages and is a bigger jump from BASIC. http://cygwin.com/ http://java.sun.com/javase/technologies/core/index.jsp ( I'm not sure how the versions compare anymore, but you could download this for example) http://java.sun.com/j2se/1.4.2/download.html Once you have a little familiarity with cygwin, I would suggest getting something like rasmol and building it yourself ( I just did this myself, much more lightweight than PyMol and combined with scripts for downloading and manipulating pdb files can actually create a useful system pretty quickly ). What is on your school's program? I would imagine some programming or computer stuff is part of your required course list. I'm asking mostly out or curiousity but it may be helpful to understand how these things are taught today. And, how is it you managed to learn BASIC "these days" withouth learning anything else? I didn't know it was that popular any more as OO seems to be taught early. I had many years of programming - starting with BASIC and assembly code on 8080 and Z80 systems running CP/M and DOS- but was out of the field for a while before learning object oriented things. I got started with Java - the Sun tutorials should be more than enough for anyone with a programming background. I downloaded the Chime plugin and was amazed at the wireframe rotating DNA- probably not impressive to anyone here but really struck me at the time. Someone at work got me going with cygwin- really great tool for learning or real stuff. Comparing scripts to "real languages" for efficacy ( sorry, too much biotech...) is very difficult. I'm not sure if Sun will ever be able to beat C++. The last time I checked, the Intel compiler and tools were pretty good at dealing with architecture or providing optimization options. I had written a hand-coded assembler routine to do a wavelet transform that used all kinds of special observations about the specific transform and the machine architecture(registers, caches, pipelining, etc) . By the time I was done, VTune and the wall clock results suggested the naively written C++ code, compiled with Intel's version 6, wre pretty similar. My point is that the compiler seems to know a lot about the CPU and I'm not sure if Sun's hotspot or related technologies can compete ( aside from the overhead time of doing runtime optimizations). If you need to write code that reflects the CPU architecture or is cache aware, this is easier in C++ as opposed to java. The Java runtime removes all memory allocations issues from the programmer and has a somewhat unpredictable garbage collector. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message _________________________________________________________________ The MSN Entertainment Guide to Golden Globes is here. Get all the scoop. http://tv.msn.com/tv/globes2007/?icid=nctagline2 From idoerg at burnham.org Mon Jan 15 16:30:29 2007 From: idoerg at burnham.org (Iddo Friedberg) Date: Mon, 15 Jan 2007 13:30:29 -0800 Subject: [BiO BB] Hello need info In-Reply-To: References: Message-ID: <45ABF275.3010808@burnham.org> pathan khan wrote: > Hello > > I have generated a few ESTs from my experiments and have some questions to > be addressed...I will be very happy to get suggestions and Help in this > regard.. > > 1. do contigs similar in base composition correspond to the same gene? If by "base composition" you mean the frequency of each base, then the answer is "no". If you mean base sequence, then the answer is "probably yes", although paralogs or low complexity sequences might give you a false positive. if > not what could be the possible explanation? Explanation for what? Similar base composition? Many genes can have similar ATGC ratios, especially in the same organism. It doesn't really mean much in this context. > > 2.Why are my ESTs not showing Hits with the already deposited ESTs of the > same organism although the protein for which they are coding are identical > but from different organisms. This question seems to be self contradictory. At the beginning you say that your ESTs are from the "same organism", but then you say that the "protein[s] for which they are coding" are from a different organism. Which is it? In any case, many ESTs in the NCBI dbEST only partially cover an organism's transcriptome. So it may be that you simply cloned ESTs that were not deposited in NCBI. -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA T: +1 858 646 3100 x3516 http://iddo-friedberg.org http://BioFunctionPrediction.org From drinep at cs.rpi.edu Wed Jan 17 14:44:25 2007 From: drinep at cs.rpi.edu (Petros Drineas) Date: Wed, 17 Jan 2007 14:44:25 -0500 Subject: [BiO BB] CFP, SDM07 Biomedical Informatics, Apr 2007 Message-ID: <000f01c73a6f$e7cad8c0$5933d580@RENSSELAFB94E5> [Apologies if you receive this more than once] Announcement and call for papers: Data Mining for Biomedical Informatics, a full-day workshop, to be held in conjunction with the 7th SIAM International Conference on Data Mining (SDM 2007) in Minneapolis, MN on April 28, 2007. For detailed information about the workshop see http://www.cs.rpi.edu/DMBIO/. Biology is rich in data, and is getting richer all the time. Deriving "big pictures from this sea of biomedical data" is a major scientific challenge that will require the close collaboration of computer scientists, biologists, and mathematicians. This workshop will provide a venue to facilitate more interaction between the SIAM Data Mining community and the numerous organizations that generate biomedical data, in order to promote joint research on topics that are relevant to both communities. We expect this workshop to attract a mixture of academics and data mining practitioners, whose focus is the analysis of biomedical data. Submitted papers should have a maximum length of six (6) pages. Papers must have an abstract of no more than 200 words. Brief survey articles, that expose the results of more than one paper to an interdisciplinary audience and that are relevant to the goals of the workshop, are particularly encouraged. Important dates: Paper submissions: Friday, February 2, 2007 Notification: Monday, February 12, 2007 Camera ready: Monday, February 19, 2007 Workshop organizers: Petros Drineas (Rensselaer Polytechnic Institute), Vipin Kumar (University of Minnesota), Michael W. Mahoney (Yahoo! Research) From henry.lenzi at gmail.com Sat Jan 20 09:53:33 2007 From: henry.lenzi at gmail.com (Henry Lenzi) Date: Sat, 20 Jan 2007 12:53:33 -0200 Subject: [BiO BB] Python or Perl In-Reply-To: <45AAC5A6.7040704@talktalk.net> References: <45AAC5A6.7040704@talktalk.net> Message-ID: <8b4c81f0701200653u33449aeao90276c2042911f47@mail.gmail.com> On 1/14/07, tim wrote: > Hi, > I am a final year Molecular Sciences student (chemistry and molecular > biology) and am trying to teach myself some bioinformatics programming. > My history is in Basic from years ago. Because of this, I find Python a > bit easier to understand. Having said this, is biopython widely used, or > would I be as well persevering with learning Perl, and then bioperl > which seems to have a bigger following? > Here's my 2 cents: you'll find more books for Perl. As a beginner, that's important. If I were you, I would look at Perl. You want to learn by examples. There's also more of a tradition in Perl, I believe (but tradition is meaningless). > Just one more question. Are most people involved in bioinformatics > programming working in industry/academia , are are there people > involved in open access , internet based projects? - just curious! > > Tim > I only know people from academia. Never heard of open access, internet based projects. This probably has to do with the fact that bioinformatics tries to tackle problems with real biological/medical significance. Usually, you work in a team with biologists or doctors. Cheers, Henry From aloraine at gmail.com Sun Jan 21 01:11:59 2007 From: aloraine at gmail.com (Ann Loraine) Date: Sun, 21 Jan 2007 00:11:59 -0600 Subject: [BiO BB] Python or Perl In-Reply-To: <8b4c81f0701200653u33449aeao90276c2042911f47@mail.gmail.com> References: <45AAC5A6.7040704@talktalk.net> <8b4c81f0701200653u33449aeao90276c2042911f47@mail.gmail.com> Message-ID: <83722dde0701202211of7111cr20b6746943f0cc61@mail.gmail.com> Hi, Here are my two cents: If it's fair to compare computer languages with human languages, then perl is English, and Python is esperanto. I've used perl and python both. During my postdoc and later at my first couple of jobs, I wrote a lot of Perl code for building Web pages (CGI) and for data-processing/mining tasks. My fellow programmers were all using Perl, so I just went along with what they were doing. After about five years of that, I decided to try out Python. I wanted to take advantage of some functionality I could get from python's 're' (regular expression) object that I couldn't so easily get from Perl. I think what attracted me to Python was how easy it was to get an re object to give me all matches in a given string, or something like that. Back then it only took me a couple of days to learn it well enough to get work done, i.e., learning the syntax, figuring out how to configure my system, setting up emacs, and so on. I think that for total beginners, python takes less time to learn than perl, and other people's Python code is generally easier to understand because the syntax is more limited and generally seems less freaky. When I was first learning Perl (after already having learned Java), I was a bit put off by having to put punctuation signs in front of variable names and also by all the weird-seeming global variables like $_ and so on. With python, it seems as though you have to keep less stuff in your head, and that let's you focus on the logic of what you're trying to do rather than remembering a lot of arcana. Both perl & python have pretty much all the third-party tools you would be likely to need -- code for talking to databases (e.g., MySQLdb) and XML handling, for example. Biopython has parsers for blast reports and reading fasta records, plus most of the other functionality of bioperl. (But I could be wrong on the latter point -- it's been years since I knew bioperl well.) Python's interactive interpreter makes programming a lot easier. You define functions in files called "modules", load them into into the interpreter environment using import or reload, and then run them. If you forget all the variables you've defined, you just run the "dir" command. You can also write a "main" method if you want and run script-like programs that way, but I hardly ever do that. The interpreter makes it easier to do science, because you can read data into the environment and interact with it. You don't have to re-write and re-run your scripts (as with Perl) every time you want to answer a simple question about a data structure. These days, it seems plain wrong to me to build up a data structure in memory and then lose it once the program terminates. Writing and using new object classes is also nicer in Python than in Perl, but again, this may have changed since I last worked with Perl. (I think I stopped using it around Perl5 or so.) It's nice to to be able to cope with both languages, of course, because sometimes you run across some-one else's code that you might want to use, and you might need to modify it. Also, there's a very nice Oreilly book on blast that has a lot of perl code examples. A fun exercise for people who know both would be to translate the examples into python. Good luck and don't forget that computing should be fun!!! Ann -- Ann Loraine, Assistant Professor Departments of Genetics, Biostatistics, Computer and Information Sciences Associate Scientist, Comprehensive Cancer Center University of Alabama at Birmingham http://www.transvar.org 205-996-4155 From abhishek.vit at gmail.com Sun Jan 21 04:30:23 2007 From: abhishek.vit at gmail.com (Abhishek Pratap) Date: Sun, 21 Jan 2007 15:00:23 +0530 Subject: [BiO BB] [ISCB-SC-RSG] Welcome to RSG-INDIA, an initiative of ISCB-SC. Message-ID: *ISCB-SC Regional Student Group in INDIA * ISCB-SC Regional Student Group for India (RSG-India) welcomes you to the Indian wing of ISCB-Student Council. RSG-India is an ISCB-SC initiative to provide a platform for students to gain exposure in the field of computational biology. RSG-INDIA was initiated by Saraswathi S., of ISCB-SC with the help of many volunteer student delegates who showed great interest in forming this group. RSG-India was formed with the blessings of Dr Michael Gribskov, Chairman ISCB, during the 5th International Conference on Bioinformatics (INCOB 2006, Dec18th-20th) held at The Ashok, New Delhi *Mission*** RSG-INDIA, in its current form is looking forward to expand its member base and attain sustainability. It has adopted the mission of ISCB-SC to develop next generation pioneers in the field of computational biology. *Benefits and Services* ? RSG-INDIA will be on the lookout for training opportunities in the form of college projects and internships for young enthusiasts in the field of computational biology.** ? Nurture a network of contacts among students and with industries, academics and local government that have an active interest in computational biology. ? Forum for discussion of the problems faced in projects and internships. ? Access to database of relevant contacts and information. ? Free subscription to ISCB's quarterly newsletter. This is a volunteer service provided *by students for the benefit of students*. Hence we would like to enlist your cooperation and enthusiastic participation in all the activities carried on by RSG-India. The protem committee for structuring the RSG-INDIA has been formed with Abhishek Pratap as the chairperson and N A. Arivarasu as the secretary. After the formal setup of the group, there will be annual elections to elect future leaders. Abhishek Pratap Protem Chairman RSG-INDIA For Student Council: http://iscbsc.org Interim Group Website: *http://groups-beta.google.com/group/rsg-india* -- ----------------------------- Abhishek Pratap Third Year Bioinformatics School of Biotechnology & Chemical Eng VIT University Ph: (91)-416-3206020 Mob: (91)-9843181010 http://bioinfosolutions.com From lixue at iastate.edu Sun Jan 21 10:14:37 2007 From: lixue at iastate.edu (Xue, Li) Date: Sun, 21 Jan 2007 09:14:37 -0600 (CST) Subject: [BiO BB] Python or Perl Message-ID: <371492101070200@webmail.iastate.edu> Hi, Look at this book on Perl: Learning Perl, 3rd Edition, By Randal L. Schwartz and Tom Phoenix (This is an excellent introduction book for persons who have never used Perl in their life:) Li > On 1/14/07, tim wrote: > > Hi, > > I am a final year Molecular Sciences student (chemistry and molecular > > biology) and am trying to teach myself some bioinformatics programming. > > My history is in Basic from years ago. Because of this, I find Python a > > bit easier to understand. Having said this, is biopython widely used, or > > would I be as well persevering with learning Perl, and then bioperl > > which seems to have a bigger following? > > > > Here's my 2 cents: you'll find more books for Perl. As a beginner, > that's important. If I were you, I would look at Perl. You want to > learn by examples. > There's also more of a tradition in Perl, I believe (but tradition is > meaningless). > > > Just one more question. Are most people involved in bioinformatics > > programming working in industry/academia , are are there people > > involved in open access , internet based projects? - just curious! > > > > Tim > > > > I only know people from academia. Never heard of open access, internet > based projects. This probably has to do with the fact that > bioinformatics tries to tackle problems with real biological/medical > significance. Usually, you work in a team with biologists or doctors. > > Cheers, > > Henry > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Xue, Li Bioinformatics and Computational Biology Iowa State University, Ames, IA 50011 515-520-1676 From landman at scalableinformatics.com Mon Jan 22 00:23:21 2007 From: landman at scalableinformatics.com (Joe Landman) Date: Mon, 22 Jan 2007 00:23:21 -0500 Subject: [BiO BB] Python or Perl In-Reply-To: <45AAC5A6.7040704@talktalk.net> References: <45AAC5A6.7040704@talktalk.net> Message-ID: <45B44A49.3030706@scalableinformatics.com> Hi Tim: tim wrote: > Hi, > I am a final year Molecular Sciences student (chemistry and molecular > biology) and am trying to teach myself some bioinformatics programming. > My history is in Basic from years ago. Because of this, I find Python a > bit easier to understand. Having said this, is biopython widely used, or > would I be as well persevering with learning Perl, and then bioperl > which seems to have a bigger following? (Caution: comments below come from a 'hardcore' Perl guy) Use the language that fits you best. What I used to joke about Perl was that I could write my Perl in Fortran. Or Basic. Or even something that looked moderately like assembler (if you take a code, pull its core out, rework it as hand tuned assembler that you teach yourself in order to get more speed for an experiment control, you understand the simultaneous thrill and awe of the forces at your control ... even more so the first time you disable all interrupts, and send the system into an infinite loop .... ) One thing I like about Perl is that it really isn't too hard to get your mind around, get productive quickly. This is good and bad. The bad part is when you realized what you were doing when you started learning it, and that there were/are far more elegant ways of expressing ones self. Ann made a comment about english and esperanto. I am not sure I got it (simplicity of expression)? Python offers lots. It gives people who use it a relatively rigid world view (IMO) that helps contain the almost free-form world view of "there is more than one way to do it" within perl. I have heard that as the biggest reason why people have switched to Python from Perl. Then again, I have heard that reasons people have switched the other way have to do with the richness and power of expression in the language, the CPAN library, see http://search.cpan.org (I had asked a while ago if there was anything similar for Python ... as of a few years ago there may have been, but nothing of the size or utility of Perl's). You can run Perl in debugger consoles if you wish, as you can with Python. You can natively export objects to permanent storage for later retrieval. I personally use the Komodo IDE and debugger. The nice thing is that it works fine for Perl, Python, Ruby, and others. Makes a handy XML folding editor too. The part that took me longest to get in Perl were regular expressions. If you don't grasp them, think of a terse semi-mathematical language you can use to describe something. This language is extraordinarily powerful. I wrote a parser for fasta files originally in about 12-20 lines of Perl. Once I understood regular expressions well enough, the parser portion was a single line. A more comprehensible single line. One thing that turned me off to Fortran (and other rigid formatted languages) was that one good turn with a paragraph reformatter and your new code just increased information entropy in the universe. At least these days, in Fortran, it has a saner non-rigid mode. Having used Fortran for somewhat more than 10 years before picking up perl, and written parsers and other nice things in it (Fortran), I am not too keen on getting back to it. This may be my own bias showing through. The most important thing that (I would hope) employers look for are not specific language skills, but the ability to learn new things, languages, techniques, and apply them. In "real time". When I look for technical people, I want to see evidence of non-rigid thinking. I want to see the ability to take a concept and do something productive with it. The language used is, to a degree, just a vehicle for expression of the solution to the problem concept, and the elegance or lack thereof that is demonstrated in wielding it *may be* secondary. Not always, but sometimes how you say it (to a computer) isn't really as important as what you are saying (to the computer). Put another way, the important thing is not necessarily what you use but how you use it. The tool needs to fit you and your goals. There are languages out there that appear to be in search of a problem to solve. There are languages out there that rapidly let you solve problems. Python and Perl belong to the latter group. As does Ruby (which I have heard people describe as a Perlization of Lisp or something like that). > > Just one more question. Are most people involved in bioinformatics > programming working in industry/academia , are are there people > involved in open access , internet based projects? - just curious! > > Tim > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Joseph Landman, Ph.D Founder and CEO Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://www.scalableinformatics.com phone: +1 734 786 8423 fax : +1 734 786 8452 or +1 866 888 3112 cell : +1 734 612 4615 From felipe.albrecht at gmail.com Mon Jan 22 15:50:51 2007 From: felipe.albrecht at gmail.com (Felipe Albrecht) Date: Mon, 22 Jan 2007 17:50:51 -0300 Subject: [BiO BB] blast alert soft In-Reply-To: <005001c71953$dcf85270$3372668a@Bioinfo1> References: <005001c71953$dcf85270$3372668a@Bioinfo1> Message-ID: Hi. What I think: uses a bio-perl or bio-python, and the result of the blast search you put into a hashtable structure and save it. Next time, you execute and compare iterating across the new result set, for each result, you see if exist into previous search, if dont exist, is a new sequences. For execute 2 approaches are possibles: put your script into cron or execute then like a deamon, and after the job, you "[u]sleep(time)" the script. If a new sequence was found, you can sends a email to your local user using "mail" software. The syntax I dont remember now and I'm using windows now. These are my 2 cents, if you want, we can talk by email and do this script together. Bye and good luck. Felipe Albrecht On 12/6/06, Johann JOETS wrote: > Hi ! > I'm looking for software that can run blast search from time to time > automatically and alert user when new homologous sequence appears. It > would be better if it could be installed locally. > Thanks for your suggestions ! > Regards. > > Johann JOETS > UMR de Genetique Vegetale > Ferme du Moulon > 91 190 Gif sur Yvette France > 33(0)169332378 > > > > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From henry.lenzi at gmail.com Tue Jan 23 15:12:20 2007 From: henry.lenzi at gmail.com (Henry Lenzi) Date: Tue, 23 Jan 2007 18:12:20 -0200 Subject: [BiO BB] Python or Perl In-Reply-To: <8b4c81f0701200653u33449aeao90276c2042911f47@mail.gmail.com> References: <45AAC5A6.7040704@talktalk.net> <8b4c81f0701200653u33449aeao90276c2042911f47@mail.gmail.com> Message-ID: <8b4c81f0701231212x2ebdc24bv3b2dc370cef916f3@mail.gmail.com> On 1/20/07, Henry Lenzi wrote: > On 1/14/07, tim wrote: > > Hi, > > I am a final year Molecular Sciences student (chemistry and molecular > > biology) and am trying to teach myself some bioinformatics > Here's my 2 cents: you'll find more books for Perl. Just to make it clear: I was specifically mentioning more books about teaching _bioinformatics_ with Perl. I don't know of a single book that teaches bioinforatics with Python. Cheers, Henry From idoerg at burnham.org Tue Jan 23 23:39:47 2007 From: idoerg at burnham.org (Iddo Friedberg) Date: Tue, 23 Jan 2007 20:39:47 -0800 Subject: [BiO BB] Python or Perl In-Reply-To: <8b4c81f0701231212x2ebdc24bv3b2dc370cef916f3@mail.gmail.com> References: <45AAC5A6.7040704@talktalk.net> <8b4c81f0701200653u33449aeao90276c2042911f47@mail.gmail.com> <8b4c81f0701231212x2ebdc24bv3b2dc370cef916f3@mail.gmail.com> Message-ID: <45B6E313.7060404@burnham.org> A freely available Biopython course given at the Pasteur Institute. Very methodical and comprehensive. Starts from Python basics. Moves on to Biopython. Includes exercises & solutions. http://www.pasteur.fr/recherche/unites/sis/formation/python/index.html Henry Lenzi wrote: > On 1/20/07, Henry Lenzi wrote: >> On 1/14/07, tim wrote: >> > Hi, >> > I am a final year Molecular Sciences student (chemistry and molecular >> > biology) and am trying to teach myself some bioinformatics >> Here's my 2 cents: you'll find more books for Perl. > > Just to make it clear: I was specifically mentioning more books about > teaching _bioinformatics_ with Perl. I don't know of a single book > that teaches bioinforatics with Python. > > > Cheers, > > Henry > _______________________________________________ > General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -- Iddo Friedberg, Ph.D. Burnham Institute for Medical Research 10901 N. Torrey Pines Rd. La Jolla, CA 92037, USA T: +1 858 646 3100 x3516 http://iddo-friedberg.org http://BioFunctionPrediction.org From drlivesa at email.uncc.edu Thu Jan 25 11:02:37 2007 From: drlivesa at email.uncc.edu (Dennis Livesay) Date: Thu, 25 Jan 2007 11:02:37 -0500 Subject: [BiO BB] Chemistry Central Journal is now accepting submissions Message-ID: Dear Colleague, I am writing to let you know that Chemistry Central Journal, a revolutionary open access peer-reviewed, online journal, has been launched and is now accepting submissions. As a journal section editor (you can see the editorial board here ) I sincerely hope that you will consider submitting your next manuscript to the journal. Chemistry Central Journal is the first international open access journal that covers all of chemistry. The journal covers research in all areas of chemistry, including analytical, biological, environmental, industrial, inorganic, organic, physical and theoretical chemistry as well as materials science, and is divided into over fifty subject areas . Of particular interest to this audience may be the Biochemistry, Biomacromolecules, Biotechnology, and Cheminformatics/Molecular Modeling subject areas. Chemistry Central Journal offers rapid, high quality peer-review, an efficient online submission process, no color charges or limits on the number of figures, and immediate publication upon acceptance. Figures can be submitted in ChemDraw (.CDX) or ISIS/Draw (.TGF) file formats. Chemistry Central Journal is working with PubChem in order that structures are deposited directly into the database. All articles will be deposited in PubMed Central, and will therefore be automatically linked into PubChem. Chemistry Central Journal is published by Chemistry Central , part of BioMed Central Ltd, the pioneering biomedical open access publisher. In order to cover the cost of publication while allowing articles to be fully open access, an article-processing charge (currently ?800) is payable for articles accepted for publication in the journal. If the submitting author's organization is a BioMed Central member , the cost of the article processing charge is covered by the membership, and no further charge is payable. For authors whose institutions are supporter members of BioMed Central a discounted article processing charge is payable by the author. Chemistry Central Journal is now accepting submissions , and expects to publish its first articles soon. Please submit your manuscript via the online submission system >. For more information about the journal you can contact me, or visit the journal website or consult the information for authors . To keep up to date with the latest articles from Chemistry Central Journal, why not register to receive article alerts when new research is published? Yours sincerely, Dennis Livesay ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Dennis R. Livesay Associate Professor Bioinformatics | Computer Science University of North Carolina at Charlotte Phone: 704.687.7995; Fax: 704.687.6610 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From jeff at bioinformatics.org Thu Jan 25 16:12:03 2007 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 25 Jan 2007 16:12:03 -0500 Subject: [BiO BB] ANNOUCE: The 7th Annual BiOAM @ Bio-IT World Conference & Expo Message-ID: <45B91D23.2010207@bioinformatics.org> Bioinformatics.Org's 7th Annual BiOAM Bio-IT World Conference & Expo World Trade Center, Boston, Massachusetts (US) April 30-May 2, 2007 The Bioinformatics Organization's Annual Meeting (BiOAM) is once again being hosted by the fine people at Cambridge Healthtech's Bio-IT World. Come and join us for our 7th organizational meeting, which is also the 5th anniversary for the Bio-IT World Conference & Expo. Our primary event this year is our Benjamin Franklin Award: a humanitarian and bioethics award presented annually by the Bioinformatics Organization to an individual who has, in his or her practice, promoted free and open access to the materials and methods used in the life sciences. The Award will be presented during the Event followed by a presentation of the recipient highlighting their research work. Time is running out to take advantage of the Early Bird Savings. If you can register by January 26th (tomorrow!), you can save up to $500. HIGHLIGHTS: Spanning three days, the meeting includes parallel conference tracks dedicated to IT Infrastructure, Discovery Informatics, Computational Science, and e-Clinical Research. Here are just some of the highlights for this year's event: Co-located User Group: Don't miss the 8th International Oracle Life Sciences User Group Meeting, taking place April 30. Four Pre-Conference Workshops: Finance and Venture Capital, Partnerships and Technologies, Semantic Web, and Future of EDC. Expanded Exhibit Hall: Featuring over 70 companies showcasing their products and services. We have a booth this year, so drop by and see some of the guys at Bioinformatics.Org during exhibit hall hours. Scientific Posters: Present a Scientific Poster and benefit from dedicated poster hours, a poster competition and a $50 savings off your conference registration. Best of Show Awards: Spotlighting new products at the expo, that demonstrate exceptional technology and innovation in research, discovery and development and clinical trials. Attend the awards ceremony or look for the Best of Show logo to find the "must-see" products on the show floor. FOR MORE INFORMATION: Website: http://www.Bio-ITWorldExpo Agenda: http://www.bio-itworldexpo.com/download_brochure2007.asp Register: https://commerce22.datapipe.com/chidb/2007/bioitworldconference/reg.asp Final agenda: http://www.bio-itworldexpo.com/download_brochure2007.asp Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 508 890 8600 -- From ykalidas at gmail.com Mon Jan 29 08:30:27 2007 From: ykalidas at gmail.com (Kalidas Yeturu) Date: Mon, 29 Jan 2007 19:00:27 +0530 Subject: [BiO BB] program for comparison of binding sites Message-ID: <5632703b0701290530vebe8d7aqc8e6ddf762ab063@mail.gmail.com> Hi I am looking for stand-alone program to compare two given binding sites. SiteBase is a web based utility. Also if I can get open source (C) program it would be better. Please suggest me relevant material. -- Kalidas Y http://ssl.serc.iisc.ernet.in/~kalidas From christoph.gille at charite.de Mon Jan 29 09:24:44 2007 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Mon, 29 Jan 2007 15:24:44 +0100 (CET) Subject: [BiO BB] program for comparison of binding sites In-Reply-To: <5632703b0701290530vebe8d7aqc8e6ddf762ab063@mail.gmail.com> References: <5632703b0701290530vebe8d7aqc8e6ddf762ab063@mail.gmail.com> Message-ID: <36167.141.42.56.114.1170080684.squirrel@webmail.charite.de> Try this http://bioinf.charite.de/haystack/ From skhadar at gmail.com Tue Jan 30 22:19:26 2007 From: skhadar at gmail.com (Shameer Khadar) Date: Wed, 31 Jan 2007 08:49:26 +0530 Subject: [BiO BB] fastacmd - sequence retreival using "string" ? Message-ID: Dear All, Is it possible to retreive sequence(s) from a fastacmd nr database based on string qureies delimited by commas. I know it is possible with the Accession IDs, Is there any way to do it for the string query. Thanks, Shameer From MEC at Stowers-Institute.org Wed Jan 31 09:51:48 2007 From: MEC at Stowers-Institute.org (Cook, Malcolm) Date: Wed, 31 Jan 2007 08:51:48 -0600 Subject: [BiO BB] fastacmd - sequence retreival using "string" ? Message-ID: Shameer, It is unclear to me exactly what you want to do. What exactly do you mean by "string query"? Does knowing that the following two command return the same result answer your question?: > fastacmd -s 15674171,66818355 > fastacmd -s NP_268346.1,XP_642837.1 > fastacmd -s 'gi|15674171|ref|NP_268346.1,gi|66818355|ref|XP_642837.1' (note: you must quote the query to prevent the shell from trying to interpret the '|' character as pipe operator). If this does not help you, then I'm really unsure what you're after... The options that appear relevant to your need, taken from running fastacmd with --help as only option, are -s Comma-delimited search string(s). GIs, accessions, loci, or fullSeq-id strings may be used, e.g. 555, AC147927, 'gnl|dbname|tag' [String] Optional -i Input file with GIs/accessions/loci for batch retrieval [String] Optional -L Range of sequence to extract (Format: start,stop) 0 in 'start' refers to the beginning of the sequence 0 in 'stop' refers to the end of the sequence [String] Optional default = 0,0 If you want to subsequences (ranges) from a bunch of different sequences, you must make separate calls to fastacmd. The -L option will not help you for this. The -L option only allows you to specify a single range. If you use it in conjuntion with multiple comma delimited search strings, this single range option is applied equally to all of the resulting sequences. Malcolm Cook Database Applications Manager - Bioinformatics Stowers Institute for Medical Research - Kansas City, Missouri > -----Original Message----- > From: > bio_bulletin_board-bounces+mec=stowers-institute.org at bioinform > atics.org > [mailto:bio_bulletin_board-bounces+mec=stowers-institute.org at b > ioinformatics.org] On Behalf Of Shameer Khadar > Sent: Tuesday, January 30, 2007 9:19 PM > To: General Forum at Bioinformatics.Org > Subject: [BiO BB] fastacmd - sequence retreival using "string" ? > > Dear All, > > Is it possible to retreive sequence(s) from a fastacmd nr > database based on > string qureies delimited by commas. > I know it is possible with the Accession IDs, Is there any > way to do it for > the string query. > > Thanks, > Shameer > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From skhadar at gmail.com Wed Jan 31 12:45:49 2007 From: skhadar at gmail.com (Shameer Khadar) Date: Wed, 31 Jan 2007 23:15:49 +0530 Subject: Fwd: [BiO BB] fastacmd - sequence retreival using "string" ? In-Reply-To: References: Message-ID: Dear Malcom, Thanks for such a detialed reply !!! I am sorry for the 'bad description' of my problem. I am aware that fastacmd -s can search using the Accession ID (say a set of numbers ), I am looking for an option to quickly search the nr database to retreive sequence basesd on the "Query String". For example : If the following is a snippet of a sequence from nr : > gi|15674171|ref|NP_268346.1,gi|Homo Sapiens - Kinase 1 MTHSTCC..... I need to retrieve the above entries (and of course entries having similar) based on a Query string say "Homo Sapiens". I know this can be done using a Perl script, and I have coded one for myself, but I need something quick like fastacmd -s. Hope you got my question this time. Thanks for all the time you spent for me !!! -- Happy Bioinformatics Across the miles... Shameer Khadar From MEC at Stowers-Institute.org Wed Jan 31 17:44:14 2007 From: MEC at Stowers-Institute.org (Cook, Malcolm) Date: Wed, 31 Jan 2007 16:44:14 -0600 Subject: [BiO BB] fastacmd - sequence retreival using "string" ? Message-ID: fastacmd will not do this for you since formatdb does not index by anything other than the sequence identifier(s). To set up free text indexing on the deflines of the fasta database you might look at Lucegene (http://www.gmod.org/?q=node/83), though the overhead may be bigger than the advantage you get from it. Cheers, Malcolm Cook > -----Original Message----- > From: > bio_bulletin_board-bounces+mec=stowers-institute.org at bioinform > atics.org > [mailto:bio_bulletin_board-bounces+mec=stowers-institute.org at b > ioinformatics.org] On Behalf Of Shameer Khadar > Sent: Wednesday, January 31, 2007 11:46 AM > To: General Forum at Bioinformatics.Org > Subject: Fwd: [BiO BB] fastacmd - sequence retreival using "string" ? > > Dear Malcom, > Thanks for such a detialed reply !!! > I am sorry for the 'bad description' of my problem. > > I am aware that fastacmd -s can search using the Accession ID > (say a set of > numbers ), I am looking for an option to quickly search the > nr database to > retreive sequence basesd on the "Query String". > > For example : If the following is a snippet of a sequence from nr : > > gi|15674171|ref|NP_268346.1,gi|Homo Sapiens - Kinase 1 > MTHSTCC..... > I need to retrieve the above entries (and of course entries > having similar) > based on a Query string say "Homo Sapiens". I know this can > be done using a > Perl script, and I have coded one for myself, but I need > something quick > like fastacmd -s. > > Hope you got my question this time. > Thanks for all the time you spent for me !!! > -- > Happy Bioinformatics > Across the miles... Shameer Khadar > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From risea at cecalc.ula.ve Tue Jan 30 07:31:57 2007 From: risea at cecalc.ula.ve (risea at cecalc.ula.ve) Date: Tue, 30 Jan 2007 08:31:57 -0400 (VET) Subject: [BiO BB] Portal Iberoamericano de Bioinformatica Message-ID: <48963.150.185.138.49.1170160317.squirrel@mail.cecalc.ula.ve> Hola a todos La presente es para que ustedes contin?en visitando y participando en el "Portal Iberoamericano de Bioinform?tica", y como su nombre lo indica, es un portal focalizado en Bioinform?tica a escala Iberoamericana. El sitio web del Portal Iberoamericano de Bioinform?tica est? en: http://portal-bio.ula.ve/ Dicho portal tiene como objetivo organizar/canalizar/focalizar informaci?n en Biolog?a Computacional y Bioinform?tica con m?s de 600 mil visitas en los ?ltimos tres a?os, y un poco menos de 700 usuarios registrados en el mismo. Para ello es importante suscribirse/registrase en el portal para estar informado y tener acceso a dicha informaci?n, y solo tomar? un minuto para ello. Visite el siguiente enlace web para suscribirse al portal: http://portal-bio.ula.ve/user. Recuerden que se pueden registrar en el enlace del portal, y el enlace web es: http://portal-bio.ula.ve/ Cordiales saludos Ra?l Isea ******************************************************************** Dr. Raul Isea | Corporaci?n Parque Tecnol?gico Centro de Calculo Cientifico | de M?rida Universidad de Los Andes | Email: risea at cecalc.ula.ve | Av. 4 Edif. General Masini, Piso 3 58-(0)274-240-3028 | M?rida, 5101, Venezuela http://www.cecalc.ula.ve/risea | Mirror Email: lrisea at yahoo.com ********************************************************************* From Daniele.Santoni at caspur.it Tue Jan 30 14:44:22 2007 From: Daniele.Santoni at caspur.it (Daniele Santoni) Date: Tue, 30 Jan 2007 20:44:22 +0100 Subject: [BiO BB] reg exp protein domain Message-ID: <20070130194423.0A4BA533EE@smtp.caspur.it> Hi everybody I?m finding regular expressions of the best known eukaryotic protein domains in the PROSITE format: F-[IVFY]-G-[LM]-M-[G>] (TACHYKININ Accession number: PS00267) or better in UNIX format. Thanks in advance Dan From skhadar at gmail.com Wed Jan 31 12:43:19 2007 From: skhadar at gmail.com (Shameer Khadar) Date: Wed, 31 Jan 2007 23:13:19 +0530 Subject: [BiO BB] fastacmd - sequence retreival using "string" ? In-Reply-To: References: Message-ID: Dear Malcom, Thanks for such a detialed reply !!! I am sorry for the 'bad description' of my problem. I am aware that fastacmd -s can search using the Accession ID (say a set of numbers ), I am looking for an option to quickly search the nr database to retreive sequence basesd on the "Query String". For example : If the following is a snippet of a sequence from nr : > gi|15674171|ref|NP_268346.1,gi|Homo Sapiens - Kinase 1 MTHSTCC..... I need to retrieve the above entries (and of course entries having similar) based on a Query string say "Homo Sapiens". I know this can be done using a Perl script, and I have coded one for myself, but I need something quick like fastacmd -s. Hope you got my question this time. Thanks for all the time you spent for me !!! -- Happy Bioinformatics Across the miles... Shameer Khadar On 1/31/07, Cook, Malcolm wrote: > > Shameer, > > It is unclear to me exactly what you want to do. What exactly do you > mean by "string query"? > > Does knowing that the following two command return the same result > answer your question?: > > > fastacmd -s 15674171,66818355 > > fastacmd -s NP_268346.1,XP_642837.1 > > fastacmd -s 'gi|15674171|ref|NP_268346.1,gi|66818355|ref|XP_642837.1' > > (note: you must quote the query to prevent the shell from trying to > interpret the '|' character as pipe operator). > > If this does not help you, then I'm really unsure what you're after... > > The options that appear relevant to your need, taken from running > fastacmd with --help as only option, are > > -s Comma-delimited search string(s). > GIs, accessions, loci, or fullSeq-id strings may be used, > e.g. 555, AC147927, 'gnl|dbname|tag' [String] Optional > -i Input file with GIs/accessions/loci for batch > retrieval [String] Optional > -L Range of sequence to extract (Format: start,stop) > 0 in 'start' refers to the beginning of the sequence > 0 in 'stop' refers to the end of the sequence [String] Optional > default = 0,0 > > If you want to subsequences (ranges) from a bunch of different > sequences, you must make separate calls to fastacmd. The -L option will > not help you for this. The -L option only allows you to specify a > single range. If you use it in conjuntion with multiple comma delimited > search strings, this single range option is applied equally to all of > the resulting sequences. > > Malcolm Cook > Database Applications Manager - Bioinformatics > Stowers Institute for Medical Research - Kansas City, Missouri > > > > -----Original Message----- > > From: > > bio_bulletin_board-bounces+mec=stowers-institute.org at bioinform > > atics.org > > [mailto:bio_bulletin_board-bounces+mec=stowers-institute.org at b > > ioinformatics.org] On Behalf Of Shameer Khadar > > Sent: Tuesday, January 30, 2007 9:19 PM > > To: General Forum at Bioinformatics.Org > > Subject: [BiO BB] fastacmd - sequence retreival using "string" ? > > > > Dear All, > > > > Is it possible to retreive sequence(s) from a fastacmd nr > > database based on > > string qureies delimited by commas. > > I know it is possible with the Accession IDs, Is there any > > way to do it for > > the string query. > > > > Thanks, > > Shameer > > _______________________________________________ > > General Forum at Bioinformatics.Org - > > BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > _______________________________________________ > General Forum at Bioinformatics.Org - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >