BioTorrents http://www.biotorrents.net/ Bioinformatics4GNU GPLThis contains all OS binaries from hmmer.org: Source: [Download: 3.9MB] MD5: 4a3d8e217556e8ea791d5eaeafb3b072 with Linux/Intel ia32 binaries: [Download: 11.3MB] MD5: 5e1f2be91122f4a15a7b9c2b6d895564 with Linux/Intel x86_64 binaries: [Download: 13.1MB] MD5: c6d42075d2bbd85227f051ad8306c185 with MacOSX/Intel binaries: [Download: 8.2MB] MD5: a2a91de34b263e8a6d8336439dcf8447 Briefly, to compile from source: % tar zxf hmmer-3.0rc2.tar.gz % cd hmmer-3.0rc2 % ./configure % make % make check The 'make check' is optional; it runs a test suite. All the binary tarballs include source code, plus a binaries/ directory containing precompiled binaries. Installing HMMER takes nothing other than moving these binaries wherever you want them. We believe HMMER compiles and runs on any POSIX-compliant system with an ANSI C99 compiler, including Mac OS/X, Linux, and any UNIX. For more installation and configuration options, see the Installation chapter of the User Guide (included in the package, and also linked below). HMMER 3.0rc2 release notes: HMMER 3.0 release candidate 2 http://hmmer.org/ SRE, Sat Mar 6 11:37:47 2010 We are counting down to the first release of HMMER 3.0, after a year of alpha and beta testing. This is release candidate two (3.0rc2). H3 is ready for production use. Indeed, it has been stable for many months. It is already widely deployed in its beta test versions for Pfam, Interpro, and other protein databases. We are still not entirely happy with a number of issues, including the state of the documentation and the range of different formats (especially alignment formats) we read. And it would be nice if we’d finished the manuscripts describing how H3 works. But all this work will just have to continue. Differences in 3.0rc2 relative to the previous 3.0rc1 release: Two reported bugs have been fixed: * #h78 phmmer –acc segfaults when no accession is available * #h77 hmmalign corrupts column before an all-deleted column Other improvements: * The test suite has expanded. * An error in man page documentation for hmmbuild –symfrac is fixed. * Portability to various UNIXen is improved, notably IBM AIX systems. * ./configure now handles –disable-{sse,vmx,dummy} properly. http://www.biotorrents.net/details.php?id=51&hit=1 Bioinformatics1GNU LGPLTaverna is an open source family of tools for designing and executing workflows, created by the myGrid project and funded through the OMII-UK. The family consists of the Taverna Engine (the workhorse), and the Taverna Workbench (desktop client) and Taverna Server (remote workflow execution server) that sit on top of the Engine. Downloaded from: http://www.taverna.org.uk/download/taverna-2-1/ md5: 8880417678c334901ee64ac849ab203f sha1: fb12ef8f68a33d903d1ed7c4c75caacb58bcb655 http://www.biotorrents.net/details.php?id=49&hit=1 Metagenomics0This is the dataset produced by the research associated with the manuscript: Qin et al. A human gut microbial gene catalogue established by metagenomic sequencing, Nature, 2010 http://www.nature.com/nature/journal/v464/n7285/abs/nature08821.html Dataset originally downloaded from: http://www.bork.embl.de/~arumugam/Qin_et_al_2010/ http://www.biotorrents.net/details.php?id=48&hit=1 Metagenomics0These are all f the sequence files, quality scores, reference genome sequences, BLAST output, and script files that were used for the project described in Morgan et al., 2010, Metagenomic Sequencing of an in vitro-Simulated Microbial Community. http://www.biotorrents.net/details.php?id=47&hit=1 Bioinformatics4GNU GPLProfile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis. After a year of alpha and beta testing, HMMER3 is ready. Release candidate 1 is available for download as a tarball. It includes precompiled binaries for Intel/Linux systems, both 64-bit (x86_84) and 32-bit (ia32) platforms, and you may just copy these into some directory in your $PATH if you like. If the precompiled versions don't work for you, you can always compile your own version from the source. Downloaded: Feb, 10, 2010 Website: http://hmmer.janelia.org/ More Information: http://selab.janelia.org/people/eddys/blog/?p=263 Orginal Source: ftp://selab.janelia.org/pub/software/hmmer3/hmmer-3.0rc1.tar.gz http://www.biotorrents.net/details.php?id=42&hit=1 Genomics0Mauve.Genome.Alignment.2.3.1.Linux-OpenSci Homepage: http://gel.ahabs.wisc.edu/mauve/ Operating System: GNU/Linux License: GNU General Public License (GPL) http://www.gnu.org/licenses/gpl.html See Also: http://sourceforge.net/projects/mauve/ Releaser: OpenSci http://twitter.com/opensci Distributor: Mininova http://mininova.org "Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics. Aligning whole genomes is a fundamentally different problem than aligning short sequences. Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the amount of sequence being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours." http://www.biotorrents.net/details.php?id=41&hit=1 Miscellaneous0GNU GPLSource code for Biotorrents (www.biotorrents.net) as of January 8, 2010 (svn revision 137). This work is licensed under the GNU GPL. http://www.biotorrents.net/details.php?id=40&hit=1 Password Protected0503 bacterial families were generated for 85 bacterial representative genomes, they have unversality of >=70. 56 of them can be phylogenetic markers the zip file is password protected (password posted to iseem internal website) it inlcude sequences, alignments and hmms for all the 503 families http://www.biotorrents.net/details.php?id=39&hit=1 Genomics0Genomic Encyclopedia of Bacteria and Archaea (GEBA) The GEBA project is aimed at systematically filling in the gaps in sequencing along the bacterial and archaeal branches of the tree of life. Though the wide variety of microbial sequencing projects undertaken throughout the world has created a rich, diverse collection of microbial genomes, strong biases in what has been sequenced thus far are evident. This project represents the first systematic attempt to use the tree of life itself as a guide to sequencing target selection. http://www.jgi.doe.gov/programs/GEBA/ Files GEBA.con: DNA sequences of contigs from 56 GEBA genomes GEBA.faa: peptide sequences of all the predicted genes from the 56 GEBA genomes GEBA.seq: DNA sequences of all the predicted genes from the 56 GEBA genomes http://www.biotorrents.net/details.php?id=38&hit=1 Bioinformatics0JCVI.Cloud.BioLinux.2009.09.18.IMG.ZIP-OpenSci Homepage: https://sourceforge.net/projects/jcvicloud/ Alternate Download: https://sourceforge.net/projects/jcvicloud/files/JCVI-Cloud-BioLinux.zip/download Distributor: Mininova http://mininova.org Release Group: OpenSci http://twitter.com/OpenSci JCVI Cloud BioLinux image enables scientists to quickly provision computation infrastructures supporting bioinformatics using cloud computing platforms such as Amazon EC2 and Eucalyptus. Upon deployment users will have instant access to a host of software including BLAST, glimmer, hmmer, phylip, rasmol, genespring, clustalw, the Celera Assembler, and the EMBOSS collection of utilities. JCVI Cloud BioLinux is built on a 64-bit instance of Ubuntu virtual server customized with bioinformatics packages from the BioLinux repository, and will be updated periodically. http://www.biotorrents.net/details.php?id=36&hit=1 Bioinformatics0## About This is the Flatfile version of ComboDB. It contains the sequance and attributes of all completed genomes. For more information, go to edhar.genomecenter.ucdavis.edu/~sbhatnagar/ComboDB/index.php ## Usage Unzip the file as tar -xvf * Use routine shel scripts or Folder viewer to navigate through. http://www.biotorrents.net/details.php?id=35&hit=1 Bioinformatics0## About This is the MySQL version of ComboDB. It contains just the attributes of all completed genomes and it's contigs and CDS in an easy to query format. For more information, go to edhar.genomecenter.ucdavis.edu/~sbhatnagar/ComboDB/index.php ## Usage Use the restore feture of youyr MySQL installation to load the database. http://www.biotorrents.net/details.php?id=34&hit=1 Genomics0This contains *only* the Pfam-A.hmm and Pfam-B.hmm files from Pfam release 24. If running Hmmer3 these are the only files you need. Instructions for use with HMMER -gunzip Pfam-A* -hmmpress Pfam-A.hmm -hmmpress Pfam-B.hmm -hmmscan Pfam-A.hmm your_fasta_file.faa Files were downloaded from: ftp://ftp.sanger.ac.uk/pub/databases/Pfam/releases/Pfam24.0/ Release notes from Pfam FTP site: PFAM : Multiple alignments and profile HMMs of protein domains RELEASE 24.0 -------------------------------------- 1. INTRODUCTION Pfam is a collection of protein family alignments which were constructed semi-automatically using hidden Markov models (HMMs). Sequences that are not covered by Pfam are clustered and aligned automatically, and released as Pfam-B. Pfam families have permanent accession numbers and contain functional annotation and cross-references to other databases, while Pfam-B families are re-generated at each release and are unannotated. 2. LOCATIONS Pfam is available on the web at: http://pfam.sanger.ac.uk/ http://pfam.cgb.ki.se/ http://pfam.janelia.org/ http://pfam.jouy.inra.fr/ http://pfam.ccbb.re.kr/ 3. STATISTICS Pfam Pfam-B ----------------------- ----------------------- Release Date families sequences residues families sequences residues Source ------- ----- -------- --------- ---------- -------- --------- --------- --------- 0.2 01/96 100 10431 2246421 11763 32081 9200334 Swiss 32 1.0 04/96 175 15610 3560959 11929 31931 8957230 Swiss 33 2.0 03/97 527 28170 6770529 13289 31349 8224614 Swiss 34 2.1 10/97 527 28205 6790960 13289 31349 8224614 Swiss 34 3.0 06/98 806 99043 22766133 33550 79544 20648530 Swiss 35 + SP-TrEMBL 5 3.1 09/98 1313 114750 27573470 33550 79544 20648530 Swiss 35 + SP-TrEMBL 5 3.2 10/98 1344 115155 27689081 33550 79544 20648530 Swiss 35 + SP-TrEMBL 5 3.3 12/98 1390 119420 28085438 33550 79544 20648530 Swiss 35 + SP-TrEMBL 5 3.4 01/99 1407 119963 28343136 33550 79544 20648530 Swiss 35 + SP-TrEMBL 5 4.0 05/99 1465 147347 34476183 128689 123610 33470292 Swiss 37 + SP-TrEMBL 9 4.1 07/99 1488 148195 34692597 36739 89640 22510097 Swiss 37 + SP-TrEMBL 9 4.2 08/99 1664 155979 36683193 40017 99587 24062200 Swiss 37 + SP-TrEMBL 9 4.3 09/99 1815 161833 37803491 39506 97492 23115975 Swiss 37 + SP-TrEMBL 9 4.4 11/99 2000 164412 38411490 39200 96055 22552453 Swiss 37 + SP-TrEMBL 9 5.0 01/00 2008 178110 41516321 39228 96077 22506088 Swiss 38 + SP-TrEMBL 11 5.1 02/00 2015 179782 41704446 42357 103709 24762358 Swiss 38 + SP-TrEMBL 11 5.2 03/00 2128 181068 42018555 42163 102843 24471000 Swiss 38 + SP-TrEMBL 11 5.3 05/00 2216 183695 42512479 41974 102024 23952537 Swiss 38 + SP-TrEMBL 11 5.4 06/00 2290 185251 42659663 41885 101728 23774015 Swiss 38 + SP-TrEMBL 11 5.5 09/00 2478 190302 43837632 41232 99302 22716640 Swiss 38 + SP-TrEMBL 11 6.0 01/01 2697 258321 59332756 40681 96571 21789591 Swiss 39 + SP-TrEMBL 14 6.1 03/01 2727 260202 59586847 40230 96128 21545422 Swiss 39 + SP-TrEMBL 14 6.2 04/01 2773 260570 59749821 58924 131100 30096444 Swiss 39 + SP-TrEMBL 14 6.3 05/01 2847 261546 60210817 58539 130194 29602298 Swiss 39 + SP-TrEMBL 14 6.4 05/01 2866 262071 60508404 58297 129257 29370968 Swiss 39 + SP-TrEMBL 14 6.5 06/01 2929 264276 61192015 57891 127861 28892585 Swiss 39 + SP-TrEMBL 14 6.6 08/01 3071 267598 61976627 57477 126378 28143196 Swiss 39 + SP-TrEMBL 14 7.0 01/02 3360 409136 93681071 78233 179966 39684197 Swiss 40 + SP-TrEMBL 18 7.1 03/02 3621 413112 94740523 77733 178097 38784346 Swiss 40 + SP-TrEMBL 18 7.2 04/02 3735 417711 95253221 77408 177141 38445765 Swiss 40 + SP-TrEMBL 18 7.3 05/02 3849 419102 95460308 83108 193509 41854966 Swiss 40 + SP-TrEMBL 18 7.4 07/02 3882 419360 95369593 83166 193462 41907032 Swiss 40 + SP-TrEMBL 18 7.5 08/02 4176 424307 96575650 82343 190360 40849796 Swiss 40 + SP-TrEMBL 18 7.6 09/02 4463 428237 97335169 81669 187725 40073352 Swiss 40 + SP-TrEMBL 18 7.7 10/02 4832 435353 99654093 80001 182610 38092326 Swiss 40 + SP-TrEMBL 18 7.8 11/02 5049 437970 100096164 79427 181013 37469930 Swiss 40 + SP-TrEMBL 18 8.0 02/03 5193 626452 142233861 76370 174607 35686841 Swiss 40.31 + SP-TrEMBL 22.0 9.0 05/03 5722 705698 160653012 98158 232641 46847522 Swiss 41.0 + SP-TrEMBL 23.0 10.0 07/03 6190 733829 167492698 96550 227325 45381141 Swiss 41.10 + SP-TrEMBL 23.15 11.0 10/03 7255 805978 184093744 94757 220445 43457201 Swiss 41.25 + SP-TrEMBL 24.14 12.0 01/04 7316 898590 205356517 108951 262041 53933483 Swiss 42.5 + SP-TrEMBL 25.6 13.0 04/04 7426 899152 205367676 108119 260253 53251778 Swiss 42.12 + SP-TrEMBL 25.12 14.0 05/04 7459 903115 206720690 107460 259106 52378429 Swiss 43.2 + SP-TrEMBL 26.2 15.0 08/04 7503 1105589 251318620 140216 357340 70848731 Swiss 44.0 + SP-TrEMBL 27.0 16.0 10/04 7677 1164599 264667462 139134 353883 69591421 Swiss 44.5 + SP-TrEMBL 27.5 17.0 03/05 7868 1321755 297821068 129746 336353 63302856 Swiss 46.0 + SP-TrEMBL 29.0 18.0 07/05 7973 1426410 322176782 128469 327279 61569471 Swiss 47.0 + SP-TrEMBL 30.0 19.0 11/05 8183 1728628 391195934 127296 322743 60022455 Swiss 48.1 + SP-TrEMBL 31.1 20.0 04/06 8296 2062824 468403714 126439 319735 59164603 Swiss 48.9 + SP-TrEMBL 31.9 21.0 11/06 8957 2343023 532701643 186970 403510 71601041 Swiss 50.0 + SP-TrEMBL 33.0 22.0 06/07 9318 2990695 679928271 182493 472700 87434067 Swiss 51.7 + SP-TrEMBL 34.7 23.0 07/08 10340 3925943 890618067 223403 1029669 215585168 Swiss 54.5 + SP-TrEMBL 37.5 24.0 07/09 11912 7079739 1627712293 142303 940849 171679060 Swiss 57.6 + SP-TrEMBL 40.6 NCBI pfam ----------------------- Release Date families sequences residues seq coverage res coverage Source ------- ----- -------- --------- ---------- ------------ ------------ ------ 23.0 07/08 10305 8334719 1674388721 66.39% 50.93% rel162 24.0 08/09 11883 11223814 2279289638 69.51% 53.60% rel172 Metaseq pfam ----------------------- Release Date families sequences residues seq coverage res coverage ------- ----- -------- --------- ---------- ------------ ------------ 23.0 07/08 6438 3055905 448190722 46.21% 33.47% 24.0 07/08 7841 4388839 705254062 66.37% 53.66% 4. CONSTRUCTION OF PFAM Pfam is based on a sequence database called Pfamseq - Pfamseq 24 is based on UniProt 15.6 (Swiss-Prot 57.6 and SP-TrEMBL 40.6). These databases can be accessed at: ftp://ftp.ebi.ac.uk/pub/databases/swissprot/release/ ftp://ftp.ebi.ac.uk/pub/databases/trembl/ Pfamseq 24 contains 9421015 sequences and 3060696203 residues. Metaseq is a collection of metagenomic sequence sample sets that contains 6612632 sequences and 1314268346 residues. NCBI non redundant sequence database release 172 contains 16146658 sequences and 4252521171 residues. Pfam-B has been constructed using ADDA. 5. DESCRIPTION OF CHANGES FROM RELEASE 23.0 to 24.0 Release 24.0 contains a total of 11912 families, with 1808 new families and 236 families killed since the last release. 75.15% of all proteins in Pfamseq contain a match to at least one Pfam domain. 53.18% of all residues in the sequence database fall within Pfam domains. Release 24.0 is the first release to be generated using HMMER3. This migration has necessitated changes in our file formats and users should be aware that HMMER3 is not backward compatible with HMMER2. For a full list of changes please view the documentation on the Pfam website. 6. FUTURE FORMAT CHANGES No major changes for the format of the flatfile planned for next release. The swisspfam file will be depracated from the next release. 7. DESCRIPTION OF RELEASE FILES relnotes.txt - This file. userman.txt - A fuller description of Pfam fields. Pfam-A.hmm - Pfam-A HMMs in an HMM library searchable with the hmmscan program. Pfam-A.seed - Annotation and seed alignments of all Pfam-A families in Pfam format. Pfam-A.full - Annotation and full alignments of all Pfam-A families in Pfam format. Pfam-A.full.ncbi - Annotation and full alignments of all Pfam-A families against NCBI genpept database. Pfam-A.full.meta - Annotation and full alignments of all Pfam-A families against metagenomic datasets. Pfam-A.fasta - A list of sequences in each Pfam-A family in fasta format. Pfam-A.dead - All Pfam-A families that have been removed from the database. Pfam-B.hmm - The first (and largest) 20,000 Pfam-B HMMs in an HMM library searchable with the hmmscan program. Pfam-B - All Pfam-B families. Pfam-C - A list of all the clans, containing annotation and lists of Pfam-A entries in the clan diff - A list of files for each family that have changed since the last release. pfamseq - The underlying sequence database in fasta format. ncbiseq - The NCBI genpept database in fasta format. metaseq - The metagenomics sequences in fasta format. swisspfam - Pfam domain organisation of all proteins in Pfamseq. 8. DESCRIPTION OF FIELDS Compulsory fields: ------------------ AC Accession number: Accession number in form PFxxxxx.version or PBxxxxxx. ID Identification: One word name for family. DE Definition: Short description of family. AU Author: Authors of the entry. SE Source of seed: The source suggesting the seed members belong to one family. GA Gathering method: Search threshold to build the full alignment. TC Trusted Cutoff: Lowest sequence score and domain score of match in the full alignment. NC Noise Cutoff: Highest sequence score and domain score of match not in full alignment. TP Type: Type of family -- presently Family, Domain, Motif or Repeat. SQ Sequence: Number of sequences in alignment. // End of alignment. Optional fields: ---------------- DC Database Comment: Comment about database reference. DR Database Reference: Reference to external database. RC Reference Comment: Comment about literature reference. RN Reference Number: Reference Number. RM Reference Medline: Eight digit medline UI number. RT Reference Title: Reference Title. RA Reference Author: Reference Author RL Reference Location: Journal location. PI Previous identifier: Record of all previous ID lines. KW Keywords: Keywords. CC Comment: Comments. NE Pfam accession: Indicates a nested domain. NL Location: Location of nested domains - sequence ID, start and end of insert. Obsolete fields: ----------- AL Alignment method of seed: The method used to align the seed members. AM Alignment Method: The order ls and fs hits are aligned to the model to build the full align. 9. ACKNOWLEDGEMENTS We are grateful to the many people who contributed data: L. Aravind, Laurence Etwiller, Matthew Bashton, Peer Bork, Richard Copley, Tim Dudgeon, Anton Enright, Nicola Kerrison, Nina Mian, William Mifsud, Chris Ponting, Joerg Schultz, Val Wood, David Waterfield, Simon Moxon, Dan Haft, Owen White, Matthew Fenech, Stephen Sammut, Joanne Pollington and O. Luke Gavin as well as many others. 10. REFERENCES Papers on Pfam are listed below: i) Sonnhammer ELL, Eddy SR, Durbin R. Proteins: Structure, Function and Genetics 28:405-420 (1997). ii) Sonnhammer ELL, Eddy SR, Birney E, Bateman A, Durbin R. Nucleic Acids Research 26:320-322 (1998). iii) Bateman A, Birney E, Durbin R, Eddy SR, Finn RD, Sonnhammer ELL. Nucleic Acids Research 27:260-262 (1999). iv) Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer ELL. Nucleic Acids Research 28:263-266 (2000). v) Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer ELL. Nucleic Acids Res. 30:276-280 (2002). vi) Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR. Nucleic Acids Res. 32(1):D138-41 (2004). vii) Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A. Nucleic Acids Res. 34(Database issue):D247-251 (2006). viii) Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A. Nucleic Acids Res. 36(Database issue):D281-288 (2008). Please reference the most recent paper. 11. THE PFAM CONSORTIUM Pfam is maintained by a consortium of researchers. You can contact the Pfam consortium at: pfam-help "at" sanger.ac.uk The current members of the Pfam consortium are: Alex Bateman, Penny Coggill, Richard Durbin, Robert Finn, Jaina Mistry, John Tate: The Wellcome Trust Sanger Institute, UK. Lorenzo Cerrutti: ISREC, Switzerland. Andreas Heger: University of Oxford, UK. Erik Sonnhammer, Kristoffer Forslund: Stockholm Bioinformatics Centre, Sweden Sean Eddy, Goran Ceric: Janelia Farm Research Campus, USA 12. COPYRIGHT NOTICE Pfam - A database of protein domain family alignments and HMMs Copyright (C) 1996-2009 The Pfam consortium. This database is free; you can redistribute it and/or modify it under the terms of the GNU Library General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. In summary, you are free to redistribute *verbatim* copies of Pfam or any Pfam files in any way you like, including packaging Pfam in proprietary software, so long as your copy of Pfam retains our copyright notice and the GNU license. You may also make *modified* copies of Pfam and distribute them, but your derivative database must be freely distributed under the GNU LGPL. Many academic freeware licenses prohibit any form of commercial use. In contrast, the intent of our license is that Pfam should be freely available to both industrial and academic researchers, including the use of the Pfam database in commercial software; however, proprietary modifications of the Pfam database itself are prohibited. Proprietary modification of the Pfam database is possible only by a separate formal licensing agreement from the Pfam consortium and our host institutions. See the file GNULICENSE for the full text of the GNU Library General Public License. This database is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Library General Public License for more details. You may also obtain a copy of the GNU LGPL by writing to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. ___________________ The Pfam Consortium 2009 http://www.biotorrents.net/details.php?id=32&hit=1 Bioinformatics0--------------------------------------------------------------------- Software: BioPuppy Linux 2.0 released Submitted by Prakash Srinivasan; posted on Tuesday, November 17, 2009 --------------------------------------------------------------------- BioPuppy is an open source minimal Linux OS for bioinformatics, based on Puppy Linux. It has tremendous support from all over the world. More than 500 Universities/colleges and thousands of individuals have downloaded and are using it. And we have just released the second version, which includes updates and more bioinformatics applications. AVAILABILITY: http://www.biopuppy.org/ http://www.biotorrents.net/details.php?id=31&hit=1 Metagenomics0All metagenomic peptide sequences from CAMERA were downloaded and searched against PFAMs using hmmscan from the HMMER 3 beta 2 package. Output looks like this: # --- full sequence ---- --- best 1 domain ---- --- domain number estimation ---- # target query E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target #------------------- -------------------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- --------------------- PRK JCVI_PEP_1112677232318 2.9e-17 62.4 0.1 3.1e-17 62.3 0.1 1.0 1 0 0 1 1 1 1 - FBPase JCVI_PEP_1112677232314 6.2e-77 258.0 0.0 6.9e-77 257.8 0.0 1.0 1 0 0 1 1 1 1 - ATP_bind_3 JCVI_PEP_1112677232286 1.5e-31 108.7 0.4 2.7e-31 107.9 0.2 1.4 1 0 0 1 1 1 1 - CPSase_L_D2 JCVI_PEP_1112677232360 7.1e-55 185.3 0.0 9.2e-55 184.9 0.0 1.1 1 0 0 1 1 1 1 - CPSase_L_chain JCVI_PEP_1112677232360 1.2e-09 38.0 0.0 2.1e-09 37.3 0.0 1.3 1 0 0 1 1 1 1 - ATP-grasp JCVI_PEP_1112677232360 4.3e-06 26.5 0.0 5.7e-06 26.1 0.0 1.2 1 0 0 1 1 1 1 - GARS_A JCVI_PEP_1112677232360 8.1e-05 21.9 0.0 0.00013 21.2 0.0 1.4 1 0 0 1 1 1 1 - ... Note: data can be decompressed faster by using pbzip2 http://www.biotorrents.net/details.php?id=30&hit=1 Metagenomics0All metagenomic peptides were downloaded from CAMERA as file "node1055606926236189023.fasta". This file is orginally 44GB uncompressed, but after removal of extras in fasta header line the file is now 7.7GB (only seq id and sample id were kept in definition line). For example each sequence looks like this: >JCVI_PEP_1112677232278 /sample_id=JCVI_SMPL_1103283000053 VPFQLRFSALAVTGLSLFLAACGGDDDHHGDASDAAKPLNLQVLYTNDHHSYFEGQSFDL NLDYDANQPGGETVRLSLGGFPRIITAMNDYRDDHTLVLNNGELNGTLYFSLX instead of the original >JCVI_PEP_1112677232278 /orf_id=JCVI_ORF_1112677232277 /read_id=JCVI_READ_1099702223732 /begin=529 /end=867 /orientation=1 /5_prime_stop=TGA /5_prime_loc=496 /3_prime_stop=TGA /ttable=11 /length=113 /sample_id=JCVI_SMPL_1103283000053 /sample_name=GS048a /number_of_sites=1 /site_id_1=JCVI_SITE_GS048 /location_1="Inside Cook's Bay, Moorea, French Polynesia" /region_1="Indian Ocean" /sample_depth_1="1.3 m" /chlorophyll_density_1="0.095 (0.091 +/- 0.02) mg/M3 (Month +/- SD)" /salinity_1="35.1 ppt" /temperature_1="28.9 C" /water_depth_1="34 m" /ip_notice="This genetic information downloaded from http://camera.calit2.net may be considered to be part of the genetic patrimony of France, the country from which the sample was obtained. Users of this information agree to: (1) acknowledge France as the country of origin in any publications where the genetic information is presented and (2) contact the CBD focal point identified on the CBD website (http://www.biodiv.org/doc/info-centre.shtml) if they intend to use the genetic information for commercial purposes." VPFQLRFSALAVTGLSLFLAACGGDDDHHGDASDAAKPLNLQVLYTNDHHSYFEGQSFDLN LDYDANQPGGETVRLSLGGFPRIITAMNDYRDDHTLVLNNGELNGTLYFSLX Note: data can be decompressed faster by using pbzip2 http://www.biotorrents.net/details.php?id=29&hit=1 Genomics0--About-- MicrobeDB provides centralized storage and access to completed Archaea and Bacteria genomes that have been parsed into a MySQL database for easier access. All microbial genomes are obtained from http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi Then information at the genome project, chromosome, and gene level are parsed and stored in a MySQL database including sequences and annotations. Finally, a Perl API is provided to interface with the MYSQL database and allow easy use of the data. A presentation providing more information about MicrobeDB is online at: http://tinyurl.com/microbedb --Install-- -decompress all directories (tar -xvjf *) Note: pbzip2 was used for compression -follow instructions in microbedb/information/INSTALL http://www.biotorrents.net/details.php?id=28&hit=1 Genomics0This is a 29way genome alignment compute with the Mauve genome aligner, version 2.3.0. http://www.biotorrents.net/details.php?id=27&hit=1 Bioinformatics1GNU LGPLTaverna is a tool for designing and running web service pipelines/workflows: http://www.mygrid.org.uk/tools/taverna/ Downloaded from: http://www.mygrid.org.uk/tools/taverna/taverna-2-0/download-taverna-2-1-b2/ http://www.biotorrents.net/details.php?id=21&hit=1 Papers0Public.Library.of.Science.PLoS.Biology.2003-OpenSci Publisher: Public Library of Science Publication: PLoS Biology Year: 2003 Volume: 1 Issue: 1-3 License: http://creativecommons.org/licenses/by/2.5 Creative Commons Attribution 2.5 Source: http://www.pubmedcentral.nih.gov/about/ftp.html PubMed Central FTP Service http://journals.plos.org/ PLoS Biology PLoS Biology (eISSN-1545-7885; ISSN-1544-9173) is an open-access, peer-reviewed general biology journal published by the Public Library of Science (PLoS), a nonprofit organization of scientists and physicians committed to making the world's scientific and medical literature a public resource. New articles are published online weekly; issues are published monthly. http://www.pubmedcentral.nih.gov/about/openftlist.html PubMed Central Open Access Subset ftp://ftp.ncbi.nlm.nih.gov/pub/pmc FTP Service Source files from the PMC Open Access Subset may include: 1. A .nxml file, which is XML for the full text of the article, encoded in the NLM Journal Archiving and Interchange DTD. 2. A PDF file of the article. 3. Image files from the article, and graphics for display versions of mathematical equations or chemical schemes. 4. Supplementary data, such as background research data or videos. Source files are listed in file.list.txt for download using wget: wget --input-file=file.list.txt Distributed by http://mininova.org Mininova andhttp://opensci.info Open Science Information http://www.biotorrents.net/details.php?id=20&hit=1