From peter.d.ashton from googlemail.com Tue Apr 1 05:29:54 2008 From: peter.d.ashton from googlemail.com (peter.d.ashton@googlemail.com) Date: Tue Apr 1 10:20:16 2008 Subject: [Bio-software] Re: blast command - one hit is sufficient References: Message-ID: On Mar 31, 4:49?pm, martin.burk...@gmail.com wrote: > Hello NG, > > i'm using command line blast for searching multiple nucleotide queries > against a protein database. For each query I get a detailed output > with hits on the database surviving my cutoff value. There can be a > lot of hits for one single query. > > For my task it would be sufficient to know if there is any hit (below > the cutoff) in the database for my query at all. Once the blast search > was able to determine a hit which e-value is lower than my cutoff > value it could print this hit to the output, stop searching and > continue with the next query. > > Is some one out there, who can provide me with a simple solution using > custom command line parameters for my blastall binary? > > That's my command until now: > > /blastall -p blastx -d /path/to/swissprot -e 1e-10 -i input.fas -m 9 > > output.bla > Hi if you add -v 1 -b 1 to your command line, blastall should only report one hit, whichever output format (-m) you choose. Cheers pete > (using blastall 2.2.15) > > Thank you :-) > Martin From darek.kedra from gmail.com Tue Apr 1 15:20:28 2008 From: darek.kedra from gmail.com (darked) Date: Tue Apr 1 21:02:47 2008 Subject: [Bio-software] Re: blast command - one hit is sufficient References: Message-ID: <09aef00d-cea2-4163-94c8-48eda0897fc9@s19g2000prg.googlegroups.com> On 31 Mar, 16:49, martin.burk...@gmail.com wrote: > Hello NG, > > i'm using command line blast for searching multiple nucleotide queries > against a protein database. For each query I get a detailed output > with hits on the database surviving my cutoff value. There can be a > lot of hits for one single query. > > For my task it would be sufficient to know if there is any hit (below > the cutoff) in the database for my query at all. Once the blast search > was able to determine a hit which e-value is lower than my cutoff > value it could print this hit to the output, stop searching and > continue with the next query. > > Is some one out there, who can provide me with a simple solution using > custom command line parameters for my blastall binary? > > That's my command until now: > > /blastall -p blastx -d /path/to/swissprot -e 1e-10 -i input.fas -m 9 > > output.bla > > (using blastall 2.2.15) > > Thank you :-) > Martin I do not think that you can change the default behavior of blast (== look for all matches) without digging into C-code of the program. There is no program switch to do so. You may restrict the output with '-v 1' switch: Number of database sequences to show one-line descriptions for (V) [Integer] If you badly need to run it a bit faster you may chek the alternative blast implementations: http://openwetware.org/wiki/Wikiomics:BLAST_tutorial#BLAST_implementations darked http://openwetware.org/wiki/Wikiomics:Bioinfo_tutorial From clements from nescent.org Wed Apr 9 16:27:24 2008 From: clements from nescent.org (Dave Clements) Date: Wed Apr 9 16:43:03 2008 Subject: [Bio-software] GMOD Summer School, Application Deadline April 15 Message-ID: Hello, This is a reminder that we will start reviewing applications for the GMOD Summer School one week from today, on Wednesday, April 15. If you are interested in attending then please submit a statement of interest by the end of April 15. See http://gmod.org/GMOD_Summer_School and http://gmod.org/GMOD_Summer_School_Statement_of_Interest for more information. Please let me know if you have any questions. Thanks, Dave Clements GMOD Help Desk On Mon, Mar 24, 2008 at 1:32 PM, Dave Clements wrote: > GMOD Summer School > 11-13 July, 2008 > National Evolutionary Synthesis Center (NESCent) > Durham, North Carolina, USA > > The first GMOD Summer School (http://gmod.org/GMOD_Summer_School) will > be held July 11-13, 2008 at the National Evolutionary Synthesis Center > (NESCent), in Durham, North Carolina, USA. GMOD is a collection of > interoperable open source software components for managing genomic > data. GMOD components are used in diverse contexts, with both > emerging and established model organisms. > > The course will provide an overview of GMOD and cover these popular > components in detail: > * Chado - a modular and extensible database schema > * Apollo - genome annotation editor > * GBrowse - genome viewer > * CMap - comparative map viewer > * Community Annotation System - GMOD's most popular components in a > single system > > This is a 2 1/2 day hands-on workshop aimed at teaching new GMOD users > how to get up and running with popular GMOD components. There will > also be a concurrent 1 day session aimed at principal investigators > that will give decision makers an overview of what GMOD can do, how > the project operates, and what level of resources are needed to use > GMOD. > > The National Evolutionary Synthesis Center (NESCent, > http://nescent.org) has joined the GMOD project with the goal of > lowering the barrier to entry for research communities focused on > emerging model organisms. The GMOD Summer School is a part of this > effort. NESCent is also extending GMOD components, particularly > Chado, to better support comparative and evolutionary data. > > If you are interested in attending the GMOD Summer School please > submit a Statement of Interest before April 15, 2008. The course is > free but enrollment is limited. For application information and a > tentative program see: > > http://gmod.org/GMOD_Summer_School > > Please let me know if you have any questions, comments, or requests. > > Thanks, > > Dave Clements > GMOD Help Desk > help@gmod.org > ------------------------ > NESCent offers various courses and workshops, as well as funding > post-doctoral and sabbatical positions, working groups and other > meetings. For more information about research and training > opportunities at NESCent, visit our website at www.nescent.org. Sign > up for our quarterly electronic newsletter at > http://www.nescent.org/about/contact.php to automatically receive > information about events at NESCent. > From bach from chevreux.org Sun Apr 13 16:59:50 2008 From: bach from chevreux.org (Bastien Chevreux) Date: Sun Apr 13 17:08:13 2008 Subject: [Bio-software] MIRA 2.9.25: sequence assembly for Sanger, 454 and Solexa Message-ID: Dear all I am really pleased to announce that the MIRA 2.9.25 sequence assembler is available: http://chevreux.org/projects_mira.html MIRA 2.9.25 is quite feature complete with respect to what is planned for the 3.0 version, this release is meant as a test bed to gather feedback on usability and possible bugs from a broader audience. Highlights in comparison to 2.9.16x1: ------------------------------------- - mapping assemblies of Solexa reads now possible (first public preview, it works like a charm for my projects and should for others too, but no guarantee) - detection of SNPs (base exchanges AND indels) with Solexa reads - vastly improved command line interface with easy to use standard configurations that should be good for the majority of all assembly projects - simplified handling of hybrid assemblies (Sanger, 454, Solexa) - greatly improved repeat disentangling routines that now also allow to discriminate and assemble longer repeat stretches that have 100% identities. - speedups and memory savings for all kinds of de-novo assemblies (Sanger, 454 or Sanger and 454 hybrids). E.g., 800000 454 FLX reads can now be assembled into contigs within ~24 hours. - drastic speedups for mapping assemblies - a program call of MIRA (miraMEM) that allows for a quick estimation of memory needs for given projects. Who should download this version? Everyone using previous version from the 2.9.x development branch as well as users from the stable 2.8.x branch who want to assemble genomes up to the size of lower eukaryotes (fungi etc.). The download page also contains a quick comparison table how this version performs against the last public release and against Newbler with respect to contig building. Versions for 64bit and 32bit Linux machines can be downloaded from http://chevreux.org/mira_downloads.html Regards, Bastien From raghava from imtech.res.in Wed Apr 16 13:43:04 2008 From: raghava from imtech.res.in (Raghava) Date: Wed Apr 16 16:45:47 2008 Subject: [Bio-software] Prediction of Secretory Proteins Message-ID: Dear Friends We have developed a highly accurate method for predicting secretory proteins of malaria parasite. This method will be useful for those working on malaria. See http://www.biomedcentral.com/1471-2105/9/201/ for detail. With Regards Raghava From jd51a from mail.com Thu Apr 17 08:46:52 2008 From: jd51a from mail.com (jd51a) Date: Thu Apr 17 12:21:26 2008 Subject: [Bio-software] test sequences for alignment program Message-ID: Hi, I am CS student who is trying to optimize some alignment software (BLASTZ in particular). Not changing the algorithm , just the implementation. I was wondering what a good set of test sequences would be. Thanks for your help, -JD From amitabh_gupta07 from yahoo.co.in Thu Apr 17 05:43:45 2008 From: amitabh_gupta07 from yahoo.co.in (Amitabh Gupta) Date: Thu Apr 17 13:24:15 2008 Subject: [Bio-software] Regarding Cluster of orthologus group for viral families Message-ID: <566718.87024.qm@web94606.mail.in2.yahoo.com> Hello sir, Hope you are fine Myself Amitabh Gupta, final year BTech Biotechnology student at JIIT Uni= versity, India. In my ongoing final year project I applied pylogenetic prof= iling on proteome set of viruses belong to Flaviviridae family. For further= improvement of my approach and cross-validation of result obtained, I= need the sequnces of viral cluster of orthologus group (VOG) of Flavivirid= ae family. Please suggest me how I will get desired sequences from N= CBI because ftp of VOG not available currently. If you will provi= de me any Perl script which suitable for generating COG for viral fami lies, its really helpfull for further progress of my project. Regards, Amitabh Gupta BTech Biotechnolgy - IVth Year JIIT University, Noida <= hr size=1> Unlimited freedom, unlimited storage. [1]Get it now References 1. 3D"http://i=/ From cjfu1981 from gmail.com Fri Apr 18 00:04:41 2008 From: cjfu1981 from gmail.com (Cipher) Date: Fri Apr 18 11:25:42 2008 Subject: [Bio-software] Inquire help about DCSE format of sequences Message-ID: <9a9f70c80804172204u6a2fe866k20347eae796a2acc@mail.gmail.com> RGVhciBhbGwsCiAgICAgIEhpISBJIGFtIGEgUGguRCBzdHVkZW50IGF0IHRoZSBJbnN0aXR1dGUg b2YgSHlkcm9iaW9sb2d5LCBDaGluZXNlCkFjYWRlbXkgb2YgU2NpZW5jZXMuIEkgYW0gd3JpdGlu ZyBoZXJlYnkgdG8gaW5xdWlyZSB5b3VyIGhlbHAgb24gdGhlIHByb2JsZW0Kb2YgY29udmVydGlu ZyBnZW5lIHNxdWVuY2VzIGludG8gRENTRSBmb3JtYXQuIEkgdHJ5IHRvIHVzZSB0aGUgc29mdHdh cmUKUm5hVml6IGZvciBwcm9kdWNpbmcgc29tZSBzZWNvbmRhcnkgc3RydWN0dXJlIGRyYXdpbmdz IG9mIFJOQSBtb2xlY3VsZXMsCndoaWNoIHVzZXMgRENTRSBhbGlnbm1lbnQgZmlsZXMgYXMgYSBz dGFydC4gSG93ZXZlciwgSSBjYW5ub3QgZmluZCBhCnNvZnR3YXJlIHRvIGNvbnZlcnQgdGhlIHNl cXVlbmNlcyBpbnRvIHRoZSBEQ1NFIGZvcm1hdC4gSSBhbSByZWFsbHkgZ3JlYXRmdWwKSWYgYW55 IG9mIHlvdSBoYXZlIHVzZWZ1bCBpbmZvcm1hdGlvbiBmb3Igc3VjaCBhIHNvZnR3YXJlIHRoYXQg Y2FuIHByb3ZpZGUKdGhpcyBmdW5jdGlvbi4gVGhhbmtzIGEgbG90IQoKCkNoZW5namllIEZVCgot LSAKLS0tLS0tLS0tLS0tLS0tLQoKNyMgRG9uZ2h1IFNvdXRoIFJvYWQsIFd1aGFuLCA0MzAwNzIs IEh1YmVpLCBDaGluYaO7Ckluc3RpdHV0ZSBvZiBIeWRyb2Jpb2xvZ3ksIENBU6O7CmVtYWlsOmNq ZnUxOTgxQGdtYWlsLmNvbSA8ZW1haWwlM0FjamZ1MTk4MUBnbWFpbC5jb20+OyBjamZ1QGloYi5h Yy5jbgo=From prems.bioinfo from gmail.com Mon Apr 21 13:01:37 2008 From: prems.bioinfo from gmail.com (prems) Date: Mon Apr 21 13:03:02 2008 Subject: [Bio-software] KARUNYA UNIVERSITY(Department of Bioinformatics) Message-ID: The Department of Bioinformatics in Karunya University was started in the year 2005. The objective is to provide excellent teaching, learning including practical training, research facilities and consultancy services in the frontier areas of Bioinformatics. The course is designed to provide advanced research and industrial exposure to the students and it covers frontier areas like Biopharmaceutics, Computational Biology, Enzyme engineering, Database management systems, Development of algorithms, Machine learning approaches, Data mining and warehousing, Genomics & proteomics, Molecular modeling & drug design, Molecular phylogeny, Neural networks, Computer simulations, Systems biology, Artificial intelligence and Nanobiotechnology . Programmes offered The Department of Bioinformatics offers the following 4 years undergraduate B.Tech. Programmes and 2 years postgraduate M.Tech. Programmes B. Tech. Bioinformatics M. Tech. Bioinformatics M.Phil Bioinformatics Ph.D Bioinformatics For eligibility and other details refer www.karunya.edu From teresaigcarvalho from gmail.com Wed Apr 23 06:20:35 2008 From: teresaigcarvalho from gmail.com (teresa isabel) Date: Wed Apr 23 06:25:39 2008 Subject: [Bio-software] protein antigenic index prediction Message-ID: Hi everyone, Does anyone know where I can find a freeware tool that makes the Jameson-Wolf antigenic index prediction? Thanks From stevet from bio.fsu.edu Wed Apr 23 12:41:04 2008 From: stevet from bio.fsu.edu (Steve Thompson) Date: Wed Apr 23 14:25:43 2008 Subject: [Bio-software] Other: Accelrys petition followup Message-ID: <20080423114117.X29516@epsilon.bio.fsu.edu> Hi all - re. http://www.petitiononline.com/gcg/ A huge THANKS to all of you that signed my petition! Within the first week online I got almost 150 signatures, and John Devereux himself most recently signed it. I sent Rob Brown of Accelrys an 'official' copy of the petition and the signatures at the end of last month. However, but not surprisingly, I have yet to receive one word back from Accelrys. I realize that we can't force them to do anything, but I at least thought that they would have the courtesy to respond to it somehow. The petition did result in a news story though. GenomeWeb News' bioinformatics newsletter, BioInform, published the story on April 4th. See my copy at: http://bio.fsu.edu/~stevet/BioInformGCG.pdf Some may feel that the BioInform story suggests the petition was merely a means of influencing commercial negotiations with Accelrys regarding code release, and have nothing to do with public domain availability, but this was never my objective. It is and remains a plea not to kill the package, and in particular SeqLab, by whatever means possible, but preferably within some type of open source arrangement. Furthermore, Accelrys argues in the article that many more people have signed the petition than subscribe to the package, and that this somehow invalidates the petition. This is completely irrelevant as the GCG license has always been to an institution, allowing as many people in that institution access as wanted, not to individual investigators. Here at FSU I have supported over 100 GCG users with one GCG license over the years. June should be interesting for us all. We'll have to see if Accelrys honors their commitment to those of us with "perpetual" licenses to provide non-node-locked, non- expiring versions of the license after June 30, 2008. Time will tell. Cheers - Steve Steven M. Thompson A C T G stevet@bio.fsu.edu \-/ http://bio.fsu.edu/~stevet/cv.html /\ /--| FSU SCS / BioInfo 4U /---/ |--/ Florida State University School of \-/ Computational Science /\ /--\ 1st floor DIRAC 150G |---\ Tallahassee, Florida \---\ 32306-4120 \--| 850-644-4490 \-/ /\ 2538 Winnwood Circle /--\ Valdosta, Georgia /---| 31601-7953 |--/ 229-249-9751 From darek.kedra from gmail.com Thu Apr 24 06:39:12 2008 From: darek.kedra from gmail.com (darked) Date: Thu Apr 24 08:30:58 2008 Subject: [Bio-software] Re: protein antigenic index prediction References: Message-ID: <7828747b-7ca4-43cf-89f6-17966ddff06e@2g2000hsn.googlegroups.com> On Apr 23, 12:20 pm, teresa isabel wrote: > Hi everyone, > > Does anyone know where I can find a freeware tool that makes the > Jameson-Wolf antigenic index prediction? > > Thanks Take a look at this paper: http://bioinformatics.oxfordjournals.org/cgi/content/full/23/24/3265 Jameson-Wolf is implemented IMHO in GCG (previously $$$ now discontinued program) . A bit newer Kolaskar and Tongaonkar is implemented in 'antigenic' from EMBOSS. Hope it helps, darked http://openwetware.org/wiki/Wikiomics:Bioinfo_tutorial http://openwetware.org/wiki/Wikiomics From stevet from bio.fsu.edu Fri Apr 25 08:16:28 2008 From: stevet from bio.fsu.edu (Steve Thompson) Date: Fri Apr 25 08:56:45 2008 Subject: [Bio-software] Other: followup to Accelrys petition followup Message-ID: <20080425085739.N36764@epsilon.bio.fsu.edu> Hello all - A brief note to let you know what's happened since my posting this last Wednesday: Rob Brown of Accelrys did contact me, finally. He says, and I quote: "The petition and the subsequent BioInform article produced a significant response and generated inquiries from a number of third party companies who now wish to discuss various possibilities relating to GCG with us. We are now in the process of following up on all of those which is taking some time." So, it looks like some good has come out of the process, although this doesn't look like the open source type of arrangement that many of us hoped for. Regardless, it may mean that the package will not be dying. And, Accelrys sent me my new non-node-locked, non-expiring license key! Cheers - Steve Steven M. Thompson A C T G stevet@bio.fsu.edu \-/ http://bio.fsu.edu/~stevet/cv.html /\ /--| FSU SCS / BioInfo 4U /---/ |--/ Florida State University School of \-/ Computational Science /\ /--\ 1st floor DIRAC 150G |---\ Tallahassee, Florida \---\ 32306-4120 \--| 850-644-4490 \-/ /\ 2538 Winnwood Circle /--\ Valdosta, Georgia /---| 31601-7953 |--/ 229-249-9751 From joyjoy.nt from gmail.com Sat Apr 26 05:38:53 2008 From: joyjoy.nt from gmail.com (Jyothish NT) Date: Sat Apr 26 06:25:44 2008 Subject: [Bio-software] Inconsistent PDB file formats Message-ID: Hi, PDB files are not Perfect. Infact, using an automated program, retrieving information from a PDB file is hard as its format is not consistent. For example, the missing coordinate informarion is usually given in REMARK 465 and 470. But if we check for protein 2FL8 there is no REMARK 465 or 470, instead this missing information is written on REMARK 3 (as there are more number of missing coordinates). Also, there is an unusual numbering given for each residue (ATOM). For example, First few resudues in the sequence are given 380 to 399. then for the rest, 12 - 200. (eg : 1K4J) I would like to know if there is any program or s/w for making the PDB files perfect? Thanks, Jyothish N.T. Research Assistant 116, Dept. of Mathematics, Indian Institute of Technology Bombay, Powai, Mumbai-400076. Email : jyothish@iitb.ac.in Ph : +91-9920980148 From raghava from imtech.res.in Sat Apr 26 14:59:26 2008 From: raghava from imtech.res.in (Raghava) Date: Sat Apr 26 15:33:57 2008 Subject: [Bio-software] Subunit Vaccine Design Message-ID: <6c0c3c2b-f6f0-4f6c-84f2-0176dc92a454@u36g2000prf.googlegroups.com> Dear Colleagues We have created a database "PRRDB: A comprehensive database of Pattern-Recognition Receptors and their ligands". This database will be very useful for those working in the field of computer aided subunit vaccine or peptide design, particularity interested in designing better adjuvants based on innate immunity. Please have a look on " http://www.biomedcentral.com/1471-2164/9/180/ " With regards Raghava ====================================================== # Dr G P S Raghava, Scientist and Head Bioinformatics Centre # # Institute of Microbial Technology, Sector-39A, Chandigarh, India # # Phone: +91-172-2690557, Fax: +91-172-2690632 # # Eadd: http://www.imtech.res.in/raghava/ raghava@imtech.res.in # #===================================================== From stevet from bio.fsu.edu Sun Apr 27 19:08:49 2008 From: stevet from bio.fsu.edu (Steve Thompson) Date: Sun Apr 27 19:51:17 2008 Subject: [Bio-software] Other: another followup (apology) Message-ID: <20080427200719.B51990@epsilon.bio.fsu.edu> Hi all - I would like to offer my apology to Accelrys and its employees for suggesting that the company would not follow through on their commitment to supply non-node-locked, non-expiring license keys to all current GCG custyomers with "perpetual" licenses. As I mentioned in my last posting Accelrys is now involved in that process and I have received my new key. It was never my intent to discredit Accelrys, nor its employess. I merely had not been informed that the process was underway. I am sorry that I miswrote and hope that any hard feelings can be overcome. Thank you. Cheers - Steve Steven M. Thompson A C T G stevet@bio.fsu.edu \-/ http://bio.fsu.edu/~stevet/cv.html /\ /--| FSU SCS / BioInfo 4U /---/ |--/ Florida State University School of \-/ Computational Science /\ /--\ 1st floor DIRAC 150G |---\ Tallahassee, Florida \---\ 32306-4120 \--| 850-644-4490 \-/ /\ 2538 Winnwood Circle /--\ Valdosta, Georgia /---| 31601-7953 |--/ 229-249-9751 From teresaigcarvalho from gmail.com Wed Apr 30 07:46:05 2008 From: teresaigcarvalho from gmail.com (teresa isabel) Date: Wed Apr 30 08:12:32 2008 Subject: [Bio-software] Jameson-Wolf Antigenic Index Message-ID: <0d91c470-f448-4665-ab70-0618fe36d81a@k37g2000hsf.googlegroups.com> Does anyone know any freeware tool, or any website that uses the Jameson-Wolf antigenic algorithm? Thanks Teresa