From yjzhang at noble.org Tue Jun 1 11:46:54 2004 From: yjzhang at noble.org (Zhang, Yuanji) Date: Tue, 1 Jun 2004 10:46:54 -0500 Subject: [BiO BB] Search reverse repeat Message-ID: <6B4878EA887E6C45AAA5AAC4C6017B0E01801A94@mail-1.noble.org> Which similarity search program will align reverse repeats in the genome? For example, if I have 2 sequences, >Seq A AATCATCAATCAGCCACTACCAAAAAATGCTCTCTGGAGTTGGTTTTCTTTTATTGATAC and >Seq B CATAGTTATTTTCTTTTGGTTGAGGTCTCTCGTAAAAAACCATCACCGACTAACTACTAA Seq A and Seq B are reverse repeats to each other. BLAST does not align A and B. I can manipulate the sequences by reversing one seq and then align, but I'd like to know whether there is a program that align A and B without extra sequence manipulation. Any information is appreciated. From Austin.Tanney at arragen.com Tue Jun 1 11:53:53 2004 From: Austin.Tanney at arragen.com (Tanney, Austin) Date: Tue, 1 Jun 2004 16:53:53 +0100 Subject: [BiO BB] Search reverse repeat - Bayesian Filter detected spam Message-ID: Run BLAST ensuring that you use the "reverse complement" BLAST. I am pretty sure most versions of BLAST have this If you are just interested in BLASTing two sequences specifically against one another use this http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html Cheers Austin > -----Original Message----- > From: Zhang, Yuanji [mailto:yjzhang at noble.org] > Sent: 01 June 2004 16:47 > To: 'bio_bulletin_board at bioinformatics.org' > Subject: [SPAM] - [BiO BB] Search reverse repeat - Bayesian Filter > detected spam > > > Which similarity search program will align reverse repeats in > the genome? > For example, if I have 2 sequences, > >Seq A > AATCATCAATCAGCCACTACCAAAAAATGCTCTCTGGAGTTGGTTTTCTTTTATTGATAC > > and > > >Seq B > CATAGTTATTTTCTTTTGGTTGAGGTCTCTCGTAAAAAACCATCACCGACTAACTACTAA > > Seq A and Seq B are reverse repeats to each other. > > BLAST does not align A and B. > > I can manipulate the sequences by reversing one seq and then > align, but I'd > like to know whether there is a program that align A and B > without extra > sequence manipulation. Any information is appreciated. > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From mgollery at unr.edu Tue Jun 1 12:21:31 2004 From: mgollery at unr.edu (Martin Gollery) Date: Tue, 01 Jun 2004 09:21:31 -0700 Subject: [BiO BB] Search reverse repeat - Bayesian Filter detected spam In-Reply-To: References: Message-ID: <40BCAD0B.2000303@unr.edu> I don't believe the reverse complement idea will work, because these two sequences are reversed, but not complements. What you could do is use a script to complement them, then run Blast with reverse complement switched on. Tanney, Austin wrote: > Run BLAST ensuring that you use the "reverse complement" BLAST. I am pretty sure most versions of BLAST have this > If you are just interested in BLASTing two sequences specifically against one another use this > http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html > > Cheers > > Austin > > >>-----Original Message----- >>From: Zhang, Yuanji [mailto:yjzhang at noble.org] >>Sent: 01 June 2004 16:47 >>To: 'bio_bulletin_board at bioinformatics.org' >>Subject: [SPAM] - [BiO BB] Search reverse repeat - Bayesian Filter >>detected spam >> >> >>Which similarity search program will align reverse repeats in >>the genome? >>For example, if I have 2 sequences, >> >>>Seq A >> >>AATCATCAATCAGCCACTACCAAAAAATGCTCTCTGGAGTTGGTTTTCTTTTATTGATAC >> >>and >> >> >>>Seq B >> >>CATAGTTATTTTCTTTTGGTTGAGGTCTCTCGTAAAAAACCATCACCGACTAACTACTAA >> >>Seq A and Seq B are reverse repeats to each other. >> >>BLAST does not align A and B. >> >>I can manipulate the sequences by reversing one seq and then >>align, but I'd >>like to know whether there is a program that align A and B >>without extra >>sequence manipulation. Any information is appreciated. >>_______________________________________________ >>BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ----------- Marty's Law- the number of Bioinformatics acronyms will double every 18 months. From Austin.Tanney at arragen.com Tue Jun 1 12:48:57 2004 From: Austin.Tanney at arragen.com (Tanney, Austin) Date: Tue, 1 Jun 2004 17:48:57 +0100 Subject: [BiO BB] Search reverse repeat - Bayesian Filter detected spam Message-ID: Sorry thats completely correct... I read that quite quickly and thought it was a more simple question. These are basically two identical sequences in different orientations. You could do as Martin says and compliment them but it does beg the question... why? Are you not ignoring the biological implications? Its one thing to turn the sequence back to front on a computer but that doesnt really have much biological significance. Unless your sequence is just in the wrong orientation. > -----Original Message----- > From: Martin Gollery [mailto:mgollery at unr.edu] > Sent: 01 June 2004 17:22 > To: bio_bulletin_board at bioinformatics.org > Subject: Re: [BiO BB] Search reverse repeat - Bayesian Filter detected > spam > > > I don't believe the reverse complement idea will work, > because these two > sequences are reversed, but not complements. What you could > do is use a > script to complement them, then run Blast with reverse complement > switched on. > > Tanney, Austin wrote: > > > Run BLAST ensuring that you use the "reverse complement" > BLAST. I am pretty sure most versions of BLAST have this > > If you are just interested in BLASTing two sequences > specifically against one another use this > > http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html > > > > Cheers > > > > Austin > > > > > >>-----Original Message----- > >>From: Zhang, Yuanji [mailto:yjzhang at noble.org] > >>Sent: 01 June 2004 16:47 > >>To: 'bio_bulletin_board at bioinformatics.org' > >>Subject: [SPAM] - [BiO BB] Search reverse repeat - Bayesian Filter > >>detected spam > >> > >> > >>Which similarity search program will align reverse repeats in > >>the genome? > >>For example, if I have 2 sequences, > >> > >>>Seq A > >> > >>AATCATCAATCAGCCACTACCAAAAAATGCTCTCTGGAGTTGGTTTTCTTTTATTGATAC > >> > >>and > >> > >> > >>>Seq B > >> > >>CATAGTTATTTTCTTTTGGTTGAGGTCTCTCGTAAAAAACCATCACCGACTAACTACTAA > >> > >>Seq A and Seq B are reverse repeats to each other. > >> > >>BLAST does not align A and B. > >> > >>I can manipulate the sequences by reversing one seq and then > >>align, but I'd > >>like to know whether there is a program that align A and B > >>without extra > >>sequence manipulation. Any information is appreciated. > >>_______________________________________________ > >>BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > >>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > >> > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- > Martin Gollery > Associate Director > Center For Bioinformatics > University of Nevada at Reno > Dept. of Biochemistry / MS330 > 775-784-7042 > ----------- > Marty's Law- the number of Bioinformatics acronyms will > double every 18 > months. > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From combiofriends at yahoo.com Tue Jun 1 15:13:59 2004 From: combiofriends at yahoo.com (com bio) Date: Tue, 1 Jun 2004 12:13:59 -0700 (PDT) Subject: [BiO BB] hai Message-ID: <20040601191359.11493.qmail@web61102.mail.yahoo.com> Hello, I am looking for most evolved sequences in bacterial genome.one possible case is a string of palindrome. eg) ATGGTTCTAATCTTGGTA (like madam) what could be the other possible sequences... please post ur ideas.... with regards deepan chakravarthy n centre for biotechnology, anna university, chennai. call me at 9840186640 (PP)- ask for deepan ===== ------------------------------------------- center for biotechnology anna university chennai-25 india __________________________________ Do you Yahoo!? Friends. Fun. Try the all-new Yahoo! Messenger. http://messenger.yahoo.com/ From kalita at pikespeak.uccs.edu Mon Jun 7 21:07:07 2004 From: kalita at pikespeak.uccs.edu (J Kalita) Date: Mon, 7 Jun 2004 19:07:07 -0600 (MDT) Subject: [BiO BB] CFP: Submission deadline for BIOT-04 is June Message-ID: <55292.128.198.172.51.1086656827.squirrel@pikespeak.uccs.edu> First Biotechnology and Bioinformatics Symposium: A Community and Academic Forum Colorado Springs, Colorado September 24, 2004 URL: http://bioinfo.uccs.edu You are invited to participate in the 2004 First Biotechnology and Bioinformatics Symposium: A Community and Academic Forum (BIOT-04). The symposium's objective is to showcase research and development activities in: Bioinformatics and Computational Biology, and Biotechnology and to promote future interdisciplinary activity and research in these areas. Abstracts and papers are solicited in these two areas, broadly interpreted. Efforts that attempt to solve biology-based problems using computational, mathematical, engineering and other means are suitable. In addition, abstracts and papers dealing with community impacts of Bioinformatics, Computational Biology and Biotechnology are appropriate. Thus, abstracts and papers in areas such as technology transfer, legal, business, and social impact issues are also invited. BIOT-04 will accept abstracts and papers for either podium presentation or poster presentation. All submissions of abstracts and papers, whether for podium or poster presentation, will be reviewed. A printed preceedings will be published containing all accepted abstracts and papers. At least one author must be registered in BIOT-04 for an abstract or a paper to be included in the proceedings. The symposium will be held on September 24, 2004 in Colorado Springs. It is expected that the 2004 symposium is the first of a series of such symposia. Partial list of Topics : Analysis of complex biological systems, Artificial or synthetic biological systems, Bioenergetics, Biomedical research, Biotechnology, Cellular function, Commercial applications of biotechnology and bioinformatics, Comparative genomics, Data mining, Databases, Evolution models, Functional genomics, Genetics, Genomics, High content analysis, High performance computing, Industrial applications of biotechnolgy and bioinformatics, Legal impacts of biotechnology and bioinformatics, Mathematical and computational models of cellular systems, Mathematical models of biophysical processes, Mathematical physiology, Microarray analysis, Molecular function, Molecular sequence and structure, Neural circuits modeling, Pathways, Pattern recognition, Phylogenetics, Physiology, Population biology, Promoter analysis and discovery, Protein structure and analysis, RNAi analysis, Sequence alignments, SNPs, Social impacts of bioinformatics and biotechnology, Systems biology, Technology transfer, Theoretical and mathematical biology, Venture capital for biotechnolgy and bioinformatics industry, Visualization. Hosted by: University of Colorado at Colorado Springs (719 262 3432 & 719 262 3256) Colorado Institute for Technology Transfer and Implementation (CITTI) (719 262 3686) Location: Penrose House 1661 Mesa Ave Colorado Springs, CO 80906-4201 From vxg189 at bham.ac.uk Wed Jun 9 07:52:35 2004 From: vxg189 at bham.ac.uk (vxg189 at bham.ac.uk) Date: Wed, 9 Jun 2004 11:52:35 +0000 Subject: [BiO BB] Opening *.gbk.gz file on linux Message-ID: hi everybody, i would be very grateful to you if you could please suggest me a way of opening a file with the extension ".gbk.gz" (a genbank file). i have tried "unzip" but it doesnot work. vibhor From hchen at utmem.edu Thu Jun 10 18:24:33 2004 From: hchen at utmem.edu (hao chen) Date: Thu, 10 Jun 2004 17:24:33 -0500 Subject: [BiO BB] Opening *.gbk.gz file on linux In-Reply-To: References: Message-ID: <40C8DFA1.7030504@utmem.edu> try gunzip *.gbk.gz Hao vxg189 at bham.ac.uk wrote: >hi everybody, > >i would be very grateful to you if you could please suggest >me a way of opening a file with the extension ".gbk.gz" (a >genbank file). i have tried "unzip" but it doesnot work. > >vibhor > > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From B.A.T.Svensson at lumc.nl Fri Jun 11 02:44:35 2004 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: Fri, 11 Jun 2004 08:44:35 +0200 Subject: [BiO BB] Opening *.gbk.gz file on linux Message-ID: A file with the extension gz is compressed and can be uncompressed with: gzip -d -----Original Message----- From: vxg189 at bham.ac.uk To: bio_bulletin_board at bioinformatics.org Sent: 9-6-2004 13:52 Subject: [BiO BB] Opening *.gbk.gz file on linux hi everybody, i would be very grateful to you if you could please suggest me a way of opening a file with the extension ".gbk.gz" (a genbank file). i have tried "unzip" but it doesnot work. vibhor _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From Austin.Tanney at arragen.com Fri Jun 11 04:39:43 2004 From: Austin.Tanney at arragen.com (Tanney, Austin) Date: Fri, 11 Jun 2004 09:39:43 +0100 Subject: [SPAM] - [BiO BB] Opening *.gbk.gz file on linux - Email has different SMTP TO: and MIME TO: fields in the email addresses Message-ID: gunzip? > -----Original Message----- > From: vxg189 at bham.ac.uk [mailto:vxg189 at bham.ac.uk] > Sent: 09 June 2004 12:53 > To: bio_bulletin_board at bioinformatics.org > Subject: [SPAM] - [BiO BB] Opening *.gbk.gz file on linux - Email has > different SMTP TO: and MIME TO: fields in the email addresses > > > hi everybody, > > i would be very grateful to you if you could please suggest > me a way of opening a file with the extension ".gbk.gz" (a > genbank file). i have tried "unzip" but it doesnot work. > > vibhor > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > This e-mail is from ArraGen Ltd The e-mail and any files transmitted with it are confidential and privileged and intended solely for the use of the individual or entity to whom they are addressed. 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Registration Number NI 43067 Registered Address : Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD From steletch at biomedicale.univ-paris5.fr Fri Jun 11 04:52:08 2004 From: steletch at biomedicale.univ-paris5.fr (=?ISO-8859-1?Q?Teletch=E9a_St=E9phane?=) Date: Fri, 11 Jun 2004 10:52:08 +0200 Subject: [SPAM] - [BiO BB] Opening *.gbk.gz file on linux - Email has different SMTP TO: and MIME TO: fields in the email addresses In-Reply-To: References: Message-ID: <1086943928.6245.7.camel@bioinfo.monsteletch.org> Le ven, 11/06/2004 ? 09:39 +0100, Tanney, Austin a ?crit : > gunzip? If you are under windows or Mac, use 7-zip to open it (http://www.7-zip.org). If under any unix (but not linux) download another compressed type (.Z instead of .gz) or install the gzip programm from the GNU source. (In IRIX you'll find them in the freeware zone as an example). Stef -- Teletch?a St?phane From Austin.Tanney at arragen.com Fri Jun 11 04:58:32 2004 From: Austin.Tanney at arragen.com (Tanney, Austin) Date: Fri, 11 Jun 2004 09:58:32 +0100 Subject: [SPAM] - RE: [SPAM] - [BiO BB] Opening *.gbk.gz file on linux - Email hasdifferent SMTP TO: and MIME TO: fields in the email addresses - Email has different SMTP TO: and MIME TO: fields in the email addresses Message-ID: If you are on windows "apparently" winzip should do gunzip too http://www.gzip.org/#faq3 If you are however on Linux its easy enough. All the Linux ditros should come with GZIP packaged. If not the RPMs are easy to obtain. Austin > -----Original Message----- > From: Teletch?a St?phane [mailto:steletch at biomedicale.univ-paris5.fr] > Sent: 11 June 2004 09:52 > To: bio_bulletin_board at bioinformatics.org > Subject: [SPAM] - RE: [SPAM] - [BiO BB] Opening *.gbk.gz file > on linux - > Email hasdifferent SMTP TO: and MIME TO: fields in the email > addresses - > Email has different SMTP TO: and MIME TO: fields in the email > addresses > > > Le ven, 11/06/2004 ? 09:39 +0100, Tanney, Austin a ?crit : > > gunzip? > > If you are under windows or Mac, use 7-zip to open it > (http://www.7-zip.org). > > If under any unix (but not linux) download another compressed type (.Z > instead of .gz) or install the gzip programm from the GNU source. > > (In IRIX you'll find them in the freeware zone as an example). > > Stef > > -- > Teletch?a St?phane > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From cling at csd.uwo.ca Mon Jun 14 22:34:05 2004 From: cling at csd.uwo.ca (Charles X. Ling) Date: Mon, 14 Jun 2004 22:34:05 -0400 (EDT) Subject: [BiO BB] CFP: Special Issue in IEEE TCBB (Deadline Sept 1, 2004) Message-ID: Call for Papers IEEE Transactions on Computational Biology and Bioinformatics Special Issue on Machine Learning for Bioinformatics IEEE Transactions on Computational Biology and Bioinformatics is seeking original manuscripts for a Special Issue on Machine Learning for Bioinformatics, scheduled for publication in the early 2005 timeframe. Bioinformatics is the science of managing, analyzing, and interpreting information from biological data, sequences and structures. Advances in genome sequencing, microarrays, proteomics and functional and structural genomics have been creating a huge amount of data to be analyzed. On the other hand, machine learning (data mining) has been advancing in strides in recent years, with high impact applications in domains ranging from marketing to science. There is great potential to increase the interaction between machine learning and bioinformatics. This special issue aims to bridge the gap between machine learning and bioinformatics. We believe that machine learning will provide powerful tools for analyzing, predicting, and understanding data from gene expression, drug design and other emerging genomic and proteomic technologies. In this special issue, we encourage papers on novel machine learning algorithms (including, but not limited to, classification, regression, clustering, probabilistic learning, inductive logic programming, reinforcement learning) and applications for tasks such as: - Gene expression analysis - Mass spectroscopy - 3D structural and functional analyses - Protein/RNA structure prediction - Phylogenetics - Sequence and structural motifs - Genomics and Proteomics - Gene finding - Drug design - Text mining in Bioinformatics Authors will need to indicate their intent to submit a paper by September 1, 2004. Please submit your paper to Manuscript Central at http://cs-ieee.manuscriptcentral.com/ by this date. As an author, you are responsible for understanding and adhering to our submission guidelines (available online at http://www.computer.org/mc/tcbb/author.htm). Feel free to contact the Peer Review Supervisor, Suzanne Werner at swerner at computer.org or the guest editors if you have any questions. Important Dates - Manuscript Submission Deadline: September 1, 2004 - Notification of Final Acceptance: December 27, 2004 - Publication Date: Early 2005 Guest Editors - Ming Li, University of Waterloo, mli at math.uwaterloo.ca - Charles Ling, University of Western Ontario, cling at csd.wuo.ca - William Noble, University of Washington, noble at gs.washington.edu - Qiang Yang, Hong Kong UST, qyang at cs.ust.hk From landman at scalableinformatics.com Thu Jun 17 23:57:08 2004 From: landman at scalableinformatics.com (Joe Landman) Date: Thu, 17 Jun 2004 23:57:08 -0400 Subject: [BiO BB] ClustalX rpms available for x86_64 and x86 architectures Message-ID: <1087531027.6148.67.camel@protein.scalableinformatics.com> Folks: Dr. Ryan Golhar had developed RPMs for clustalw/clustalx . We updated the SPEC files to build independent of other RPMs, and built x86_64 and a few others. Feel free to pick up Ryan's original RPMs and the updated source and binary RPMs at http://downloads.scalableinformatics.com/downloads/clustalx/ As usual, please email feedback on the packaging or compiler bugs to us. If you have trouble with the binary RPMs, please try building from source. Joe -- Joseph Landman, Ph.D Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://scalableinformatics.com phone: +1 734 612 4615 From yjzhang at noble.org Fri Jun 18 14:03:54 2004 From: yjzhang at noble.org (Zhang, Yuanji) Date: Fri, 18 Jun 2004 13:03:54 -0500 Subject: [BiO BB] Some questions of alignment Message-ID: <6B4878EA887E6C45AAA5AAC4C6017B0E01801AA7@mail-1.noble.org> Hello Dear Colleagues, I have 2 mathmatical questions about necleotide sequence alignment: 1. Given 2 homologous sequences of the same length (L) (e.g., L = 30 nt), and mismatches (M, 0 <= M <= L) are allowed in the alignment, how many possible alignments will be? (One assumption: biologically it does not make much sense when M = L, but mathmatically, there is one possible alignment between the 2 sequences, and mismatch occurs in every position.) 2. Suppose blastn is used to detect the alignment. Given word size = 7, mismatch punishment = -1, and match reward = 1, how many alignments cannot be detected by blast? Any idea is welcome. From nuraini at cs.usm.my Sat Jun 19 02:04:03 2004 From: nuraini at cs.usm.my (Nur'Aini Abdul Rashid) Date: Sat, 19 Jun 2004 14:04:03 +0800 (Singapore Standard Time) Subject: [BiO BB] threshold value. Message-ID: <40D3D753.000006.78473@nuraini.cs.usm.my> ANybody has used cosine similarity measure between two sequence? What is the threshold value between homolog and non homolog sequence... Thanks. Nur'Aini -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 01.gif Type: image/gif Size: 2663 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: IMSTP.gif Type: image/gif Size: 494 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 01_b.jpg Type: image/jpeg Size: 5627 bytes Desc: not available URL: From cheremushkin at ngs.ru Fri Jun 18 23:02:15 2004 From: cheremushkin at ngs.ru (Evgeny Cheremushkin) Date: Sat, 19 Jun 2004 10:02:15 +0700 Subject: [BiO BB] Some questions of alignment In-Reply-To: <6B4878EA887E6C45AAA5AAC4C6017B0E01801AA7@mail-1.noble.org> References: <6B4878EA887E6C45AAA5AAC4C6017B0E01801AA7@mail-1.noble.org> Message-ID: <548263221.20040619100215@ngs.ru> Hello Yuanji, Saturday, June 19, 2004, 1:03:54 AM, you wrote: ZY> Hello Dear Colleagues, ZY> I have 2 mathmatical questions about necleotide sequence alignment: ZY> 1. Given 2 homologous sequences of the same length (L) (e.g., L = 30 nt), ZY> and mismatches (M, 0 <= M <= L) are allowed in the alignment, how many ZY> possible alignments will be? (One assumption: biologically it does not make ZY> much sense when M = L, but mathmatically, there is one possible alignment ZY> between the 2 sequences, and mismatch occurs in every position.) If alignment is defined as all possible match-mismatch combinations, then there are N=2^L possible alignments. ZY> 2. Suppose blastn is used to detect the alignment. Given word size = 7, ZY> mismatch punishment = -1, and match reward = 1, how many alignments cannot ZY> be detected by blast? As I understand: alignment is detected by blastn if L-M>0. Have to be less then 4 matches. undetected alignments number U=C(7,3)+C(7,2)+C(7,1)+1=64 N=2^7=128 ZY> Any idea is welcome. ZY> _______________________________________________ ZY> BiO_Bulletin_Board maillist - ZY> BiO_Bulletin_Board at bioinformatics.org ZY> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Best regards, Evgeny mailto:cheremushkin at ngs.ru From yjzhang at noble.org Mon Jun 21 11:47:51 2004 From: yjzhang at noble.org (Zhang, Yuanji) Date: Mon, 21 Jun 2004 10:47:51 -0500 Subject: [BiO BB] RE: Some questions of alignment Message-ID: <6B4878EA887E6C45AAA5AAC4C6017B0E01801AA9@mail-1.noble.org> Dear Evgeny, Thank you for your response. I am afraid 'alignment' was not well defined in my original post. What I really mean is the possible distribution of mismatches (M) along the length (L) of the aligned 2 sequences. Two sequences are identical Except for the positions with mismatches. So when M = 0, there is only one possible alignment, and when M = 1, there are L alignments (the mismatch can be in each of all L positions). I think the possible alignments is C(L,M) but not sure. About undetected alignments by blastn. There are several cases. Case 1 is that the mismatches are distributed in such a way that no seed alignment (7 or more nt identical) can be found. Case 2 is that the alignment score is reduced by a row of mismatches too much so that blast will not extend the alignment to include the mismatches. There might be other cases too. So the number of undetected alignments is a function of word size, patterns of mismatch distribution,and mismatch punishment and match reward scoring scheme. From kalita at rabbit.uccs.edu Mon Jun 21 15:58:41 2004 From: kalita at rabbit.uccs.edu (J. Kalita) Date: Mon, 21 Jun 2004 13:58:41 -0600 (MDT) Subject: [BiO BB] Submission deadline extended for BIOT-04 to June 28th In-Reply-To: <20040621160107.2F918D1F15@www.bioinformatics.org> References: <20040621160107.2F918D1F15@www.bioinformatics.org> Message-ID: <51880.128.198.168.173.1087847921.squirrel@www.cs.uccs.edu> Hello everyone, We had some problems with our server due to power outages in Colorado and some people had problems submitting abstracts and papers. Therefore, we are extending the submission deadline till next Monday, June 28th. The symposium is going to be held in Colorado Springs, Colorado on September 24th, 2004. Here is the call again. Jugal Kalita -------- First Biotechnology and Bioinformatics Symposium: A Community and Academic Forum Colorado Springs, Colorado September 24, 2004 URL: http://bioinfo.uccs.edu, click on "Symposium" on top left menu You are invited to participate in the 2004 First Biotechnology and Bioinformatics Symposium: A Community and Academic Forum (BIOT-04). The symposium's objective is to showcase research and development activities in: Bioinformatics and Computational Biology, and Biotechnology and to promote future interdisciplinary activity and research in these areas. Abstracts and papers are solicited in these two areas, broadly interpreted. Efforts that attempt to solve biology-based problems using computational, mathematical, engineering and other means are suitable. In addition, abstracts and papers dealing with community impacts of Bioinformatics, Computational Biology and Biotechnology are appropriate. Thus, abstracts and papers in areas such as technology transfer, legal, business, and social impact issues are also invited. BIOT-04 will accept abstracts and papers for either podium presentation or poster presentation. All submissions of abstracts and papers, whether for podium or poster presentation, will be reviewed. A printed preceedings will be published containing all accepted abstracts and papers. At least one author must be registered in BIOT-04 for an abstract or a paper to be included in the proceedings. The symposium will be held on September 24, 2004 in Colorado Springs. It is expected that the 2004 symposium is the first of a series of such symposia. Partial list of Topics : Analysis of complex biological systems, Artificial or synthetic biological systems, Bioenergetics, Biomedical research, Biotechnology, Cellular function, Commercial applications of biotechnology and bioinformatics, Comparative genomics, Data mining, Databases, Evolution models, Functional genomics, Genetics, Genomics, High content analysis, High performance computing, Industrial applications of biotechnolgy and bioinformatics, Legal impacts of biotechnology and bioinformatics, Mathematical and computational models of cellular systems, Mathematical models of biophysical processes, Mathematical physiology, Microarray analysis, Molecular function, Molecular sequence and structure, Neural circuits modeling, Pathways, Pattern recognition, Phylogenetics, Physiology, Population biology, Promoter analysis and discovery, Protein structure and analysis, RNAi analysis, Sequence alignments, SNPs, Social impacts of bioinformatics and biotechnology, Systems biology, Technology transfer, Theoretical and mathematical biology, Venture capital for biotechnolgy and bioinformatics industry, Visualization. Hosted by: University of Colorado at Colorado Springs (719 262 3432 & 719 262 3256) Colorado Institute for Technology Transfer and Implementation (CITTI) (719 262 3686) Location: Penrose House 1661 Mesa Ave Colorado Springs, CO 80906-4201 From tsucheta at hotmail.com Thu Jun 24 10:56:11 2004 From: tsucheta at hotmail.com (Sucheta Tripathi) Date: Thu, 24 Jun 2004 14:56:11 +0000 Subject: [BiO BB] program to find indels Message-ID: An HTML attachment was scrubbed... URL: From mjmccorm at mtu.edu Thu Jun 24 21:39:47 2004 From: mjmccorm at mtu.edu (Matt McCormick) Date: Thu, 24 Jun 2004 21:39:47 -0400 (EDT) Subject: [BiO BB] parsing repeatmasker .tbl files Message-ID: <1253.24.236.179.54.1088127587.squirrel@huskymail.mtu.edu> Hi, I've generated thousands of repeatmasker .tbl files. I want to be able to extract certain table information(ie filename, total_length, number of retroelements, and length occupied). Is there any bioperl documentation on doing this? I've looked at the bioperl api for Bio::Tools::RepeatMasker but it wasn't much help to me. Any suggestions? Thank you. -Matt McCormick Undergraduate in Bioinformatics Michigan Technological University http://www.bio.mtu.edu/~mjmccorm From peter.groenen at home.nl Fri Jun 25 18:27:03 2004 From: peter.groenen at home.nl (Peter Groenen) Date: Sat, 26 Jun 2004 00:27:03 +0200 Subject: [BiO BB] Ka/Ks Message-ID: <001101c45b03$8a18b100$0601a8c0@D7M9N41J> I am looking for a command line tool that can handle protein alignments as input and aligns the corresponding transcripts. I want to use it for Ka/Ks determination. Secondly, I need something like a "sliding " Ka/Ks determination to see if there is a difference within a protein when looking at smaller segments. I looked at SNAP, and also PAML but they are not very straightforward in use, especially hte diffenret formats are giving me trouble. Any ideas? Thanks in advance. Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From operon at www.ufsm.br Fri Jun 25 18:40:28 2004 From: operon at www.ufsm.br (Marcos de Carvalho) Date: Fri, 25 Jun 2004 19:40:28 -0300 Subject: [BiO BB] Ka/Ks In-Reply-To: <001101c45b03$8a18b100$0601a8c0@D7M9N41J> References: <001101c45b03$8a18b100$0601a8c0@D7M9N41J> Message-ID: Hi Peter, On Sat, 26 Jun 2004 00:27:03 +0200, Peter Groenen wrote: > I am looking for a command line tool that can handle protein alignments > as input and aligns the corresponding transcripts. I want to use it for > Ka/Ks determination. Try TRANALIGN from the EMBOSS package. http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/tranalign.html Cheers Marcos From dmnunif at charter.net Sun Jun 27 11:54:42 2004 From: dmnunif at charter.net (D. Norris) Date: Sun, 27 Jun 2004 10:54:42 -0500 Subject: [BiO BB] parsing repeatmasker .tbl files References: <1253.24.236.179.54.1088127587.squirrel@huskymail.mtu.edu> Message-ID: <000901c45c5f$0f91fa10$3b8ac418@VALUED4DA88152> Matt: Sorry, we are not able to help you.. Dale ----- Original Message ----- From: "Matt McCormick" To: Sent: Thursday, June 24, 2004 8:39 PM Subject: [BiO BB] parsing repeatmasker .tbl files > Hi, > I've generated thousands of repeatmasker .tbl files. I want to be able to > extract certain table information(ie filename, total_length, number of > retroelements, and length occupied). Is there any bioperl documentation > on doing this? I've looked at the bioperl api for > Bio::Tools::RepeatMasker but it wasn't much help to me. Any suggestions? > Thank you. > > -Matt McCormick > > Undergraduate in Bioinformatics > Michigan Technological University > http://www.bio.mtu.edu/~mjmccorm > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From dmnunif at charter.net Sun Jun 27 12:02:38 2004 From: dmnunif at charter.net (D. Norris) Date: Sun, 27 Jun 2004 11:02:38 -0500 Subject: [BiO BB] Ka/Ks References: <001101c45b03$8a18b100$0601a8c0@D7M9N41J> Message-ID: <001701c45c60$2c8b9ee0$3b8ac418@VALUED4DA88152> ----- Original Message ----- From: Peter Groenen To: bio_bulletin_board at bioinformatics.org Sent: Friday, June 25, 2004 5:27 PM Subject: [BiO BB] Ka/Ks I am looking for a command line tool that can handle protein alignments as input and aligns the corresponding transcripts. I want to use it for Ka/Ks determination. Secondly, I need something like a "sliding " Ka/Ks determination to see if there is a difference within a protein when looking at smaller segments. I looked at SNAP, and also PAML but they are not very straightforward in use, especially hte diffenret formats are giving me trouble. Any ideas? Thanks in advance. Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From dmnunif at charter.net Sun Jun 27 12:07:51 2004 From: dmnunif at charter.net (D. Norris) Date: Sun, 27 Jun 2004 11:07:51 -0500 Subject: [BiO BB] Ka/Ks References: <001101c45b03$8a18b100$0601a8c0@D7M9N41J> Message-ID: <001f01c45c60$e5d76190$3b8ac418@VALUED4DA88152> Peter: Sorry, our corporaton can not help you. Our research in bioinformatics is on the electrochemistry by which proteins transduce environmental chemical groups or energy into information in living cells or multicellular organisms. Dale ----- Original Message ----- From: Peter Groenen To: bio_bulletin_board at bioinformatics.org Sent: Friday, June 25, 2004 5:27 PM Subject: [BiO BB] Ka/Ks I am looking for a command line tool that can handle protein alignments as input and aligns the corresponding transcripts. I want to use it for Ka/Ks determination. Secondly, I need something like a "sliding " Ka/Ks determination to see if there is a difference within a protein when looking at smaller segments. I looked at SNAP, and also PAML but they are not very straightforward in use, especially hte diffenret formats are giving me trouble. Any ideas? Thanks in advance. Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From biodavidjm at yahoo.es Mon Jun 28 11:35:36 2004 From: biodavidjm at yahoo.es (=?iso-8859-1?q?David=20JM?=) Date: Mon, 28 Jun 2004 17:35:36 +0200 (CEST) Subject: [BiO BB] Bioinformatics source for urpmi? In-Reply-To: Message-ID: <20040628153536.36191.qmail@web50105.mail.yahoo.com> Hi, I'm taking the first steps with Mandrake linux (and with Bioinformatics) and I would know if there is a source with bioinformatic's packages in order to setup urpmi (http://easyurpmi.zarb.org/). It would be very very useful. It would be great! Cheers, davidjm ______________________________________________ Renovamos el Correo Yahoo!: ?100 MB GRATIS! Nuevos servicios, m?s seguridad http://correo.yahoo.es From steletch at biomedicale.univ-paris5.fr Mon Jun 28 11:50:01 2004 From: steletch at biomedicale.univ-paris5.fr (=?ISO-8859-1?Q?Teletch=E9a_St=E9phane?=) Date: Mon, 28 Jun 2004 17:50:01 +0200 Subject: [BiO BB] Bioinformatics source for urpmi? In-Reply-To: <20040628153536.36191.qmail@web50105.mail.yahoo.com> References: <20040628153536.36191.qmail@web50105.mail.yahoo.com> Message-ID: <1088437801.8158.30.camel@bioinfo.monsteletch.org> Le lun, 28/06/2004 ? 17:35 +0200, David JM a ?crit : > Hi, > > I'm taking the first steps with Mandrake linux (and > with Bioinformatics) and I would know if there is a > source with bioinformatic's packages in order to setup > urpmi (http://easyurpmi.zarb.org/). > > It would be very very useful. It would be great! > > Cheers, > > davidjm Use Main, contrib and PLF. Depending on packages you want, they may fall in one the three for licensing reasons. With the three (and may be jpackage) you should get a good overview of them. (if not complete) Stef -- http://www.steletch.org Fingerprint: 1E83 26EE A2F1 87E5 5865 4DBF F2B4 9083 F44C AE88 GPG key @ http://www.steletch.org/article.php3?id_article=13 Mandrakelinux release 10.1 (Cooker) @ http://www.mandrakesoft.com/ 17:48:34 up 8:22, 11 users, load average: 0.67, 0.86, 0.89 From landman at scalableinformatics.com Mon Jun 28 13:32:06 2004 From: landman at scalableinformatics.com (Joe Landman) Date: Mon, 28 Jun 2004 13:32:06 -0400 Subject: [BiO BB] Bioinformatics source for urpmi? In-Reply-To: <20040628153536.36191.qmail@web50105.mail.yahoo.com> References: <20040628153536.36191.qmail@web50105.mail.yahoo.com> Message-ID: <1088443924.17261.64.camel@protein.scalableinformatics.com> Hi Davidim: Try Luc's www.biolinux.org, my downloads.scalableinformatics.com, and a few others. Joe On Mon, 2004-06-28 at 11:35, David JM wrote: > Hi, > > I'm taking the first steps with Mandrake linux (and > with Bioinformatics) and I would know if there is a > source with bioinformatic's packages in order to setup > urpmi (http://easyurpmi.zarb.org/). > > It would be very very useful. It would be great! > > Cheers, > > davidjm > > > > ______________________________________________ > Renovamos el Correo Yahoo!: ?100 MB GRATIS! > Nuevos servicios, m?s seguridad > http://correo.yahoo.es > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Joseph Landman, Ph.D Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://scalableinformatics.com phone: +1 734 612 4615 From ryangolhar at hotmail.com Mon Jun 28 14:04:34 2004 From: ryangolhar at hotmail.com (Ryan Golhar) Date: Mon, 28 Jun 2004 14:04:34 -0400 Subject: [BiO BB] Bioinformatics source for urpmi? In-Reply-To: <20040628153536.36191.qmail@web50105.mail.yahoo.com> Message-ID: <00b301c45d3a$5e1e31e0$0b00a8c0@GOLHARMOBILE1> I'm in the process of constructing a bunch of RPMs (RedHat) for bioinformatics software. Some open-source, and some not open-source. I have to sift through them -- I have 53 RPMs so far of various apps and a bunch of perl modules as well... Once I finish, I'll go back and post the open-source RPM links somehwere and announce it here... Ryan -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of David JM Sent: Monday, June 28, 2004 11:36 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Bioinformatics source for urpmi? Hi, I'm taking the first steps with Mandrake linux (and with Bioinformatics) and I would know if there is a source with bioinformatic's packages in order to setup urpmi (http://easyurpmi.zarb.org/). It would be very very useful. It would be great! Cheers, davidjm ______________________________________________ Renovamos el Correo Yahoo!: ?100 MB GRATIS! Nuevos servicios, m?s seguridad http://correo.yahoo.es _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From ryangolhar at hotmail.com Mon Jun 28 19:02:48 2004 From: ryangolhar at hotmail.com (Ryan Golhar) Date: Mon, 28 Jun 2004 19:02:48 -0400 Subject: [BiO BB] Bioinformatics source for urpmi? In-Reply-To: <00b301c45d3a$5e1e31e0$0b00a8c0@GOLHARMOBILE1> Message-ID: <00c201c45d64$07b08c20$0b00a8c0@GOLHARMOBILE1> I forgot to mention the not open-source RPMs will not be posted due to licensing issues... ----- Ryan Golhar Computational Biologist The Informatics Institute at The University of Medicine & Dentistry of NJ Phone: 973-972-5034 Fax: 973-972-7412 Email: golharam at umdnj.edu -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of Ryan Golhar Sent: Monday, June 28, 2004 2:05 PM To: bio_bulletin_board at bioinformatics.org Subject: RE: [BiO BB] Bioinformatics source for urpmi? I'm in the process of constructing a bunch of RPMs (RedHat) for bioinformatics software. Some open-source, and some not open-source. I have to sift through them -- I have 53 RPMs so far of various apps and a bunch of perl modules as well... Once I finish, I'll go back and post the open-source RPM links somehwere and announce it here... Ryan -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of David JM Sent: Monday, June 28, 2004 11:36 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Bioinformatics source for urpmi? Hi, I'm taking the first steps with Mandrake linux (and with Bioinformatics) and I would know if there is a source with bioinformatic's packages in order to setup urpmi (http://easyurpmi.zarb.org/). It would be very very useful. It would be great! Cheers, davidjm ______________________________________________ Renovamos el Correo Yahoo!: ?100 MB GRATIS! Nuevos servicios, m?s seguridad http://correo.yahoo.es _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From lxyiwc at yahoo.com Tue Jun 29 12:27:47 2004 From: lxyiwc at yahoo.com (l x yi) Date: Tue, 29 Jun 2004 09:27:47 -0700 (PDT) Subject: [BiO BB] fixed alignment Message-ID: <20040629162747.88405.qmail@web52005.mail.yahoo.com> Hi, I'm studying statistical distribution for fixed local alignment scores. Does anyone know when fixed alignment (alignment given in advance) may be useful for research? How to obtain data/generate data for a numerical example/simulation on fixed alignment? Thank you very much. Lily __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From landman at scalableinformatics.com Tue Jun 29 14:17:26 2004 From: landman at scalableinformatics.com (Joe Landman) Date: Tue, 29 Jun 2004 14:17:26 -0400 Subject: [BiO BB] updated NCBI 2.2.9 RPMs Message-ID: <1088533045.16839.553.camel@protein.scalableinformatics.com> Folks: Fixed a number of problems with the spec file and with the build. Also set up a working static build, so you won't need the same libraries as I have. Makes the binaries quite a bit larger though. We are working on getting the source RPM for this and the dynamic build out later on today. You can pull the latest build from http://downloads.scalableinformatics.com/downloads/ncbi/ (as usual). These use the tarball as released from NCBI on 15-June. Note that this build corrects the performance problem on Opteron that some people had reported to us. Joe -- Joseph Landman, Ph.D Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://scalableinformatics.com phone: +1 734 612 4615 From sourangshu at csa.iisc.ernet.in Tue Jun 29 15:06:51 2004 From: sourangshu at csa.iisc.ernet.in (Sourangshu Bhattacharya) Date: Wed, 30 Jun 2004 00:36:51 +0530 Subject: [BiO BB] fixed alignment In-Reply-To: <20040629162747.88405.qmail@web52005.mail.yahoo.com> References: <20040629162747.88405.qmail@web52005.mail.yahoo.com> Message-ID: <40E1BDCB.7090402@csa.iisc.ernet.in> Hi Lily, Could you explain what exactly you mean by "fixed" local alignments ?? Thank you, Sourangshu l x yi wrote: > Hi, > I'm studying statistical distribution for fixed local alignment > scores. Does anyone know when fixed alignment (alignment given in > advance) may be useful for research? How to obtain data/generate > data for a numerical example/simulation on fixed alignment? > > Thank you very much. > > Lily > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > -- Sourangshu Bhattacharya PhD Student, Dept. of Computer Science & Automation, Indian Institute of Science, Bangalore - 560012, India. Website: http://people.csa.iisc.ernet.in/sourangshu Cell Phone : 91-98457 97492 From dmnunif at charter.net Tue Jun 29 22:29:18 2004 From: dmnunif at charter.net (D. Norris) Date: Tue, 29 Jun 2004 21:29:18 -0500 Subject: [BiO BB] Bioinformatics source for urpmi? References: <20040628153536.36191.qmail@web50105.mail.yahoo.com> Message-ID: <001101c45e4a$0b7d2c00$b878b118@VALUED4DA88152> David: Sorry, but our bioinformatics efforts focus on electrochemical parameters of biological systems. dmn ----- Original Message ----- From: "David JM" To: Sent: Monday, June 28, 2004 10:35 AM Subject: [BiO BB] Bioinformatics source for urpmi? > Hi, > > I'm taking the first steps with Mandrake linux (and > with Bioinformatics) and I would know if there is a > source with bioinformatic's packages in order to setup > urpmi (http://easyurpmi.zarb.org/). > > It would be very very useful. It would be great! > > Cheers, > > davidjm > > > > ______________________________________________ > Renovamos el Correo Yahoo!: ?100 MB GRATIS! > Nuevos servicios, m?s seguridad > http://correo.yahoo.es > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From biodavidjm at yahoo.es Wed Jun 30 05:38:34 2004 From: biodavidjm at yahoo.es (=?iso-8859-1?q?David=20JM?=) Date: Wed, 30 Jun 2004 11:38:34 +0200 (CEST) Subject: [BiO BB] Bioinformatics source for urpmi? In-Reply-To: <00b301c45d3a$5e1e31e0$0b00a8c0@GOLHARMOBILE1> Message-ID: <20040630093834.38232.qmail@web50104.mail.yahoo.com> Ryan, It will be wonderful. I'll wait here!! Cheers, davidjm (Thanks for the others answers too!) --- Ryan Golhar escribi?: > I'm in the process of constructing a bunch of RPMs > (RedHat) for > bioinformatics software. Some open-source, and some > not open-source. I > have to sift through them -- I have 53 RPMs so far > of various apps and a > bunch of perl modules as well... > > Once I finish, I'll go back and post the open-source > RPM links somehwere > and announce it here... > > Ryan > > > > -----Original Message----- > From: bio_bulletin_board-admin at bioinformatics.org > [mailto:bio_bulletin_board-admin at bioinformatics.org] > On Behalf Of David > JM > Sent: Monday, June 28, 2004 11:36 AM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] Bioinformatics source for urpmi? > > > Hi, > > I'm taking the first steps with Mandrake linux (and > with Bioinformatics) and I would know if there is a > source with bioinformatic's packages in order to > setup > urpmi (http://easyurpmi.zarb.org/). > > It would be very very useful. It would be great! > > Cheers, > > davidjm ______________________________________________ Renovamos el Correo Yahoo!: ?100 MB GRATIS! Nuevos servicios, m?s seguridad http://correo.yahoo.es From sourangshu at csa.iisc.ernet.in Wed Jun 30 07:43:01 2004 From: sourangshu at csa.iisc.ernet.in (Sourangshu Bhattacharya) Date: Wed, 30 Jun 2004 17:13:01 +0530 Subject: [BiO BB] Getting PDB id from Swissprot entry Message-ID: <40E2A745.6030400@csa.iisc.ernet.in> Hi, Is there a direct way (without reading the protein name from swissprot and searching in PDB) of getting the PDB id of the protein corresponding to a particular Swissprot id ? Also, how do I know whether structure for a particular protein corresponding to a swissprot id has been determined or not ? Thank you very much.. Regards, Sourangshu. -- Sourangshu Bhattacharya PhD Student, Dept. of Computer Science & Automation, Indian Institute of Science, Bangalore - 560012, India. Website: http://people.csa.iisc.ernet.in/sourangshu Cell Phone : 91-98457 97492 From dmb at mrc-dunn.cam.ac.uk Wed Jun 30 09:32:34 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 30 Jun 2004 14:32:34 +0100 (BST) Subject: [BiO BB] Getting PDB id from Swissprot entry In-Reply-To: <40E2A745.6030400@csa.iisc.ernet.in> Message-ID: On Wed, 30 Jun 2004, Sourangshu Bhattacharya wrote: >Hi, > >Is there a direct way (without reading the protein name from swissprot >and searching in PDB) of getting the PDB id of the protein corresponding >to a particular Swissprot id ? I would use the MSD database, which maintains a manually curated version of the SwissProt to PDB mapping. >Also, how do I know whether structure for a particular protein >corresponding to a swissprot id has been determined or not ? Strictly speeking, the above mapping gives you this. More realistically, however, you can consider very close homologues to the above set as also 'solved'. Where you draw the line is a matter of requirement, but you can get reasonable models (allegedly) at > 40% sequence identity, or reasonable 'fold prediction' at much larger distances (see SUPERFAMILY for example). It all depends on what you want to do. >Thank you very much.. > >Regards, >Sourangshu. > > From idoerg at burnham.org Wed Jun 30 14:14:34 2004 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed, 30 Jun 2004 11:14:34 -0700 Subject: [BiO BB] Mandrake 10.0 and Swiss PDB viewer Message-ID: <40E3030A.9040301@burnham.org> Hi all, I recently installed Mandrake 10.0, and I an trying to run SwissPDB-Viewer, which worked fine on my RH7.3 machine. When I run the lates version (3.7sp5) I get a: /usr/share/SPDBV/bin/spdbv.Linux: error while loading shared libraries: libXm.so.3: cannot open shared object file: No such file or directory A symolic link: /usr/X11R6/lib/libXm.so.3 -> /usr/X11R6/lib/libXm.so.2.0.1 and /sbin/ldconfig did not help. Downgrading to version 3.7 I manage to run the program, but I get no test in the menu bar area, rendering spdbv pretty much useless. Changing color depth on the graphics device did not help. Help? Thanks, Iddo -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9930 http://ffas.ljcrf.edu/~iddo From cheremushkin at ngs.ru Wed Jun 23 02:12:41 2004 From: cheremushkin at ngs.ru (Evgeny Cheremushkin) Date: Wed, 23 Jun 2004 13:12:41 +0700 Subject: [BiO BB] RE: Some questions of alignment In-Reply-To: <6B4878EA887E6C45AAA5AAC4C6017B0E01801AA9@mail-1.noble.org> References: <6B4878EA887E6C45AAA5AAC4C6017B0E01801AA9@mail-1.noble.org> Message-ID: <456391085.20040623131241@ngs.ru> Hello Yuanji, Monday, June 21, 2004, 10:47:51 PM, you wrote: ZY> Dear Evgeny, ZY> Thank you for your response. I am afraid 'alignment' was not well defined in ZY> my original post. What I really mean is the possible distribution of ZY> mismatches (M) along the length (L) of the aligned 2 sequences. Two ZY> sequences are identical Except for the positions with mismatches. So when M ZY> = 0, there is only one possible alignment, and when M = 1, there are L ZY> alignments (the mismatch can be in each of all L positions). I think the ZY> possible alignments is C(L,M) but not sure. Yes, it is correct. ZY> About undetected alignments by blastn. There are several cases. Case 1 is ZY> that the mismatches are distributed in such a way that no seed alignment (7 ZY> or more nt identical) can be found. Case 2 is that the alignment score is ZY> reduced by a row of mismatches too much so that blast will not extend the ZY> alignment to include the mismatches. There might be other cases too. So the ZY> number of undetected alignments is a function of word size, patterns of ZY> mismatch distribution,and mismatch punishment and match reward scoring ZY> scheme. Please, formalize a problem mathematically. ZY> _______________________________________________ ZY> BiO_Bulletin_Board maillist - ZY> BiO_Bulletin_Board at bioinformatics.org ZY> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Best regards, Evgeny mailto:cheremushkin at ngs.ru From 3Dsig at weizmann.ac.il Sun Jun 27 04:31:21 2004 From: 3Dsig at weizmann.ac.il (3Dsig) Date: Sun, 27 Jun 2004 11:31:21 +0300 Subject: [BiO BB] 3Dsig Structural Bioinformatics Meeting, 90+ Abstracts now online + Late abstracts still accepted http://3Dsig.weizmann.ac.il/ Message-ID: <014201c45c21$20907230$e3504d84@IBM66> Dear Colleague, We would like to inform you that the 3Dsig Structural Bioinformatics Meeting (July 29-30 July 2004, Glasgow, Scotland, UK, part of the ISMB/ECCB Bioinformatics Conference) has opened all abstract material to the public. Whether you decide to come or not, you may want to view the online abstracts: http://3dsig.weizmann.ac.il/3dsig/2004/abstracts.html 3Dsig will have a novel laptop session where authors will be at their numbered stations with their laptops describing their work. The idea is to offer a semi-formal, yet intimate channel during 3Dsig to facilitate discussion of individual research. Abstracts are still accepted till June 30th. As the organization of the 3 panel discussions will be conducted in the upcoming days, you may want to send such an abstract quickly. Topics include: 3D data-mining; 3D programming modules; docking and protein-protein/ligand interaction prediction; membrane protein assembly prediction; secondary structure and domain assignment; structure-based function prediction; structural databases; structural genomics; structure prediction; structure representation; the role of geometry and energetics in protein structure and function Last, sponsors are still welcomed - see online information. Looking forward to meeting you at 3Dsig, 3Dsig organizing committee ~~~~~~~~~~~~~~~~~~~~ http://3Dsig.weizmann.ac.il/ 3Dsig at weizmann.ac.il -------------- next part -------------- An HTML attachment was scrubbed... URL: