Bug#723771: ITP: python-freecontact -- fast protein contact predictor - binding for Python
Package: wnpp Severity: wishlist Owner: Laszlo Kajan -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 * Package name: python-freecontact Version : 1.1 Upstream Author : Laszlo Kajan * URL : http://rostlab.org/ * License : GPL-3+ Programming Lang: C++, Python Description : fast protein contact predictor - binding for Python FreeContact is a protein residue contact predictor optimized for speed. Its input is a multiple sequence alignment. FreeContact can function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of DS. Marks (2011) and PSICOV of D. Jones (2011). FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. Depending on the alignment, 8-fold or higher speedups are possible. A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after-weighting) sequence count bigger than the length of the query sequence should be used. Alignments with tens of thousands of (effective) sequences are considered good input. jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite can be used to generate the alignments, for example. This package contains the Python binding. -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) iQIcBAEBAgAGBQJSOzKiAAoJEJvS1kCaDFL6J3kP/2/qfDcjegth6xBoPPM41zG2 S8aMWpSq7RZJMJ5bf/m730XNEmdRm7twEvg3Txp1r2RGqW2xda1isj8HOZHnyrUE 72pfOhzx2Eur31bKSZxdvk6gH+v8l3lCWZMewe7a3DjeGnSibEi8oNRTycpQOrOX MSXhRj8eXxYYOGHhrydrnHmTgobog3lGkRyedb3t3drUhaKhlSUN32n/xDawg9Yh HIieEqvWQxtq/4JkFQxpu59gMRxutvDtJqcxjKkgAnTB6CK3Px/XtCWMBfv1+4sH 2sHPwntSoEouLPHvtTScV4OYrs27PcXV6xvE0rAZpRzfmIfqYCz8AA4HM6HoLG8n ETxAxcSEqjKiDZqFxM+n1OazIZwtOzwlCZepy9HS3EFmluLDUekuT73jPtfSP7rf zNOJfaFnkVePZ8/ashG/0Ykn15lIK764AnZUChkLk0u2uejMIo5FN+xq3sCL5dwN Q7bFiJc/0Kgbb0ynGbK4n01aZzps54JybwTcxT+XOtcx97hBhepQ803z+rWREVNh tfGe6tSV4B2QGtX9h1sxuCXN2yAufxDIfOcFRCg/2TrkITuHsJfC8Yu/KroGX2U5 zVTeBZkkX0LVbZcn5DPWFbr1gdrgjsfoE8ImxyBqy32LL86Vmq3/KDQQdy+pkpXX rwar4214Aj2k+0770ymv =yzVT -END PGP SIGNATURE- -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130919172144.2075.87520.reportbug@debian-unstable.rostclust
Bug#723747: ITP: libfreecontact-perl -- fast protein contact predictor - binding for Perl
Package: wnpp Severity: wishlist Owner: Laszlo Kajan -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 * Package name: libfreecontact-perl Version : 0.08 Upstream Author : Laszlo Kajan * URL : http://rostlab.org/ * License : GPL-1+ or Artistic Programming Lang: C, Perl Description : fast protein contact predictor - binding for Perl FreeContact is a protein residue contact predictor optimized for speed. Its input is a multiple sequence alignment. FreeContact can function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of DS. Marks (2011) and PSICOV of D. Jones (2011). . FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. Depending on the alignment, 8-fold or higher speedups are possible. . A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after-weighting) sequence count bigger than the length of the query sequence should be used. Alignments with tens of thousands of (effective) sequences are considered good input. . jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite can be used to generate the alignments, for example. . This package contains the Perl binding. -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) iQIcBAEBAgAGBQJSOwPeAAoJEJvS1kCaDFL6OBwP/2g0nJQoCrxgbJT4M4+MdDYT puMZ0X0VAJqTipGWNawb1Xd10QFmqOSg1K8Rkou+CpO1zqssvreyhkd+53SvfL/d t6/AugvGYK222KeaOI0NA57ihHIkmJhxSvTgCSY3cKAgqks3JKZoOcxK8mi2xwlN Y2dnokBLRXLWRYvLkjyq9Ct+oFuzOIl/Mto8EviyRRkcBEYpOBfogc3mM0DlejFW wZt2rmi/qoOwOc+DIc9YisZocKx4BGNjLLq55cMbGQUF2Nm6G7rgvCezIIzwJ82r lU5tOL7Zxs5psrHEne/ocMr22jLmjrbV7yCByvmQAjUWa67rtpffnVulDrP1t6rl Oy9/vpTRJ9vPrqoV2a0F7JgBAfkMIZf1bBuuJcffXhNMvOcy80mg4CLq30nA7kmW LBaKInSxhoJd03aqj2XSRCI6wJNb2UHy1QrKapug3nt3B/pp5GcsuF4lRnEMf5Mp 2TNg1bnj95RRkUIouJrQ/PDYq0tWLpXsGB9cZFvbVEiocILpAC9T3SkpAxALm4DA pb+J8tb3V/K2CYl5trsLJOuts6A9Q40RqTZplOk3vWtgrtLsKb+IBvY5M1JzqcL6 QJfn3dc1tZPGUi60bKmQLZ+UEmrJ8ts07+iXwNxqTx1ggvy1E4g+Hqpd/oKb1EJh J02XqyW8iKuAbZDSomb+ =8w/X -END PGP SIGNATURE- -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130919140216.32507.83518.reportbug@debian-unstable.rostclust
Bug#705537: ITP: metastudent -- predictor of Gene Ontology terms from protein sequence
Package: wnpp Severity: wishlist Owner: Laszlo Kajan -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 * Package name: metastudent Version : 1.0.7 Upstream Author : Tobias Hamp * URL : https://rostlab.org/owiki/index.php/Metastudent * License : GPL-2+ Programming Lang: Perl, Python, Java Description : predictor of Gene Ontology terms from protein sequence Often, only the sequence of a protein is known, but not its functions. Metastudent will try to predict missing functional annotations through homology searches (BLAST). . All predicted functions correspond to Gene Ontology (GO) terms from the Molecular Function Ontology (MFO) and the Biological Process Ontology (BPO) and are associated with a reliability score. -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) iQIcBAEBAgAGBQJRbS5vAAoJEJvS1kCaDFL6koQP/13ADRhPTdJcqzBqIAb/sxks JuhwNADTLTcdv/hBeEDJJTei8psFIb+RjJykwV9tWJ8FoBVClQIwxyeTiMahuUfU XnazexpOZEZtaYNNBUm4fZKUVCCYr8nAcaQztfy36UksM4Bjj+NregI4o8GuR/nE 27D0D6ZKXdZaR5r9//J0ZFKp/cqqGIXxc6PeSgDLOtt/DNmRD24+o/hXllnzH+hv 6R3o0atf4s6WDa7VdGV9XrZBgyyNYEvJYp8xn5rt3JtUgyTuq0tZxjuCAvjeWnnJ LHsV+Qj5ItxS3p5y5rOomfTM0Y2WskFsdrdCwbTw75UjhboyKSUQMGSd5Hg5ecee 0hc3Qpg7GmX3zvZ7Ha1DrMxWtRCE4q0D/Ma6HOPdWlcxA/IcUHHj5MmUKmk0B0v/ oc7ADpP+WCXxuWEDmiiaajXWrdv/J3msUdUGMZJg7FvNLiHOUv6Rhec6cIZkINoW a8zcTCr92j5IPJ8dgglLgeYn/njQpkQ65j4so+T55qidjLlL+iNr51GPni30jPmu Qm9WrzEyvkghKFpylXWS2nMvvr8jxRe5VWJ5beYwwL/UeGsQ4iBKjTF2gA47d0RL kq9pbAn3OahmCuPHyBf/+NQUrkfEoBtXoe7PZOf2sNBxfzXVWf9v4iewZ6hI21sk UUXjuyw0y7tRvhZeJmeG =3RgD -END PGP SIGNATURE- -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130416105652.3386.7449.reportbug@debian-unstable.rostclust
Bug#703256: RFH: gridengine -- Distributed resource management
Package: wnpp Severity: normal -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello! I am Laszlo Kajan, a member of the 'Gridengine packaging' project [1]. This project team-maintains gridengine [2], a distributed resource management system, in Debian. gridengine used to be - well, still is on wheezy - a package of the Sun Grid Engine. Our team is now inclined to continue maintaining gridengine as one of the free forks of the Sun Grid Engine: the Son of Grid Engine (SGE) [3]. The reason is that the upstream developer, Dave Love, is giving us a lot of help with this, and is very enthusiastic about keeping Son of Grid Engine in Debian. Our team - I feel, after discussions in the team [4] - could use new members willing to go deeper into the delicacies of packaging this distributed system for Debian, and tackle the issues (see the thread in [4]). And to match Dave's pace :). If you are interested in gridengine and SGE and feel you can help, please send an email to the team mailing list at . If you would like to check out the current Debianization, please visit [5]. Contributions to this wiki page are most welcome. Best regards, Laszlo [1] https://alioth.debian.org/projects/pkg-gridengine/ [2] http://packages.debian.org/source/wheezy/gridengine [3] https://arc.liv.ac.uk/trac/SGE [4] http://lists.alioth.debian.org/pipermail/pkg-gridengine-devel/2013-March/000675.html [5] http://wiki.debian.org/GridenginePackaging/GitGuide -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) iQIcBAEBAgAGBQJRRf2SAAoJEJvS1kCaDFL6whgQAJX2codOwgIBIL47LzP0SS7d S2eqlsnkW0orminN1FAZtdmVKOAqcWnXI9utglEqtHbFxj5tsUv5L1Shja9J38Dp iDxLARrzQO39iHTv8YoVpsVeB8P7thgSX6GOFg4CF+pfSn5f3LL8TaIWC0qjA1G8 rGIjKRmlGi+O2j6IiM1M6dCUW9ek9PdlIAYHuSP36TRWD7c7PQAphnVBhp7LTg74 vr8R2AeRIZ7HxFpUf7DcL5R6pEE7DVpPEWEm7pe8/Y2/sfHsK+fTtHmtnGqWa4oi w5D1cp+soSsFQqeoCvQz8s5VxZbyuHNx7qO3+49XpERtL+sUmR3RWZLMZFbUnU7p GHLowI/DGUXuHQLxe8Fq47ihSBFIq2f/4xxfwxIgnnh39RhJ6N1ipE7as9msRcSq 5DlL63faDI73QoyHibdbYOaLAWUn+5PGMNKyDWEiArC+ziHIbeTFX4WZ0Odswq58 hkA41dToWKJU9uYvxx25e+rZqWomTRNWTG0ZT65/wzvi9cczGzH20WuFhqeQaI/+ 9siU+jXxlvFjwoCZkyctWpE5+Mfjlsvz9NanFVK3ioCRQwI90ncoae5GHhqvipLW P4eA95fdmLxHvHqQOLp0WUUzfipPXxqSkLIbRIvQe7c1v0CEHuLPFOdzXv9kNGjF wP/Wdu0fjTHQh57zopPC =bNXu -END PGP SIGNATURE- -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130317172958.17346.82994.reportbug@debian-unstable.rostclust
Bug#690058: ITP: conservation-code -- tool to score protein sequence conservation
Package: wnpp Severity: wishlist Owner: Laszlo Kajan -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 * Package name: conservation-code Version : 20110309.0 Upstream Author : John A. Capra , Mona Singh * URL : http://compbio.cs.princeton.edu/conservation/ * License : GPL-2.0+ Programming Lang: Python Description : protein sequence conservation scoring tool Enhances: concavity This package provides score_conservation(1), a tool to score protein sequence conservation. . The following conservation scoring methods are implemented: * sum of pairs * weighted sum of pairs * Shannon entropy * Shannon entropy with property groupings (Mirny and Shakhnovich 1995, Valdar and Thornton 2001) * relative entropy with property groupings (Williamson 1995) * von Neumann entropy (Caffrey et al 2004) * relative entropy (Samudrala and Wang 2006) * Jensen-Shannon divergence (Capra and Singh 2007) . A window-based extension that incorporates the estimated conservation of sequentially adjacent residues into the score for each column is also given. This window approach can be applied to any of the conservation scoring methods. . The program accepts alignments in the CLUSTAL and FASTA formats. . The sequence-specific output can be used as the conservation input for concavity. . Conservation is highly predictive in identifying catalytic sites and residues near bound ligands. -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) iQIcBAEBAgAGBQJQdEEGAAoJEJvS1kCaDFL6ABkP+gJtgskydA+sOOf5Hi9/AYvQ i30VuQUVpY5uDIrxJ+o1c66wGHIzNzvLP+IVnCSDdK0BX1tLb2QqGMGRo32jG/yE K6jpfRyRwKMiZ8hZ9tM5w78NiJt5vSWyc6unGZdIRcpEIZVBU9T2joxmxNluu4z5 PI/jXxwMSqXQNY1NuhjosRpY0F5nltFSrjQAF3SFT1QUCpEGfmZKMaxvniP3ubeg dbPqPcDE8VgZFxMIKBB+FnGGb+QIoKYrP621Vx+FRrnv23Gd8vhidYEbAsXRXU7U gVP0k+RayjuikNGeZ+Bwm00oyy8/ehXKjsufG2e/FCo/G1dW3LmA+gUw0yZQbeXK 5WDdoiVDsgzlyAqnbVljiGIHoA8a9azu5Ta2/pyyPj0a2YB16o8V4XnWDC/N6WIQ 5C4gbpc4M0tA4yP/eCFkAwVKGr8BH4REApkDR7XqzcmVXVz2xQIqnea7SSea2dTc D2bednPxJh3C4eOOvhmDT5meg82/xfCJxIRyEcLon7g7bGBveGRhVA49W/Wxitph app1tsOp4NE9m5z5yIE83ZtdLrvAhaWib63JGf+9tsDkdWzVVnHORGiCUC6TRy7t YGz3D5+fi0GHEnJF0wpu/Yk2G2TWxnZ/3sQ2IrE9/IMorYLLM+szKns5rqdff9XY 7Fdtl/aJ3vKorM1wJSqx =6Kbc -END PGP SIGNATURE- -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121009152149.2728.83411.reportbug@debian-unstable.rostclust
Bug#689020: ITP: concavity -- predictor of protein ligand binding sites from 3D structure and sequence conservation
Package: wnpp Severity: wishlist Owner: Laszlo Kajan -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 * Package name: concavity Version : 0.1 Upstream Author : Thomas Funkhouser , John A. Capra * URL : http://compbio.cs.princeton.edu/concavity/ * License : GPL-3+ Programming Lang: C++ Description : predictor of protein ligand binding sites from 3D structure and sequence conservation ConCavity predicts protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. . ConCavity takes as input a PDB format protein structure and (optionally) files that characterize the evolutionary sequence conservation of the chains in the structure file. . The following result files are produced (by default): * residue ligand binding predictions for each chain (*.scores) * residue ligand binding predictions in a PDB format file (residue scores placed in the temp. factor field, *_residue.pdb * pocket prediction locations in a DX format file (*.dx) * PyMOL script to visualize the predictions (*.pml) . ConCavity has many features. The default run of concavity is equivalent to ConCavity^L in the paper: 'Capra JA, Laskowski RA, Thornton JM, Singh M, and Funkhouser TA(2009) Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure. PLoS Comput Biol, 5(12).'. -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) iQIcBAEBAgAGBQJQZX4/AAoJEJvS1kCaDFL6WSwP/0JAWgVwepTLSRFGON9RQmZ7 r6vUpQs3GmZxPYPa+vqY961HPkG4FKXu2hywRN/dojoz+FVL9R1MHmLuU+trJJ8p tbknGUdTOYLvygrBSzAUYY1O3Vqgk9zO6ht0je5WdNSiFJiaUk/z+LezAzwvfdzd zo0wfB9CVqT72tBE3Y0fLjudBDG3HlTyiL5JnSHIvFk9E9alsYU1r04GYOIwmi38 /txTH6QspTPlOmL3Ky1IvM3oQNR+LUL/QHO1vCJ1EmrErNju4A2jWFkoe8bvGZYw tyPEr8ygzNel0+/vD1MDGF3seRJZAz10SKduxEMsT6xC8myHoXbOkKeGKceUc2wm 8rgJUZhBUGuq5jtt2g44al5ArWo82bS+qbAqJ8AYhVjF9rm8wUjGQxtObb53Si2J aW1lEYlWI+VDeUPBfpQNIa9MuwnbBGsgbp8+015g7ci7W1PO3pVx6T13an6Xl83u naw55C0flsE63W78bt0a8qKmCyFLBO485J7CdHKolR/2x8i1SGGeSoOnJRO1o1rO g0vKrcCX7Vv/2/9N88E03dGjQJLCRFb3JBOpzkYZnwyVNfqSdLmVSFSGh+Hloo2M QzmXnVpmGMnWy6aUN2zgTWUmKg39yXvajICTnBBEcsQLKvOCwvTv7ODaU9/dbHF+ kM8AxpsQLVn3kBabB4r+ =5PF/ -END PGP SIGNATURE- -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120928103900.24805.55055.reportbug@debian-unstable.rostclust
Bug#684403: ITP: python-librcsb-core-wrapper -- library that exports C++ mmCIF accessors to Python
Package: wnpp Severity: wishlist Owner: Laszlo Kajan -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 * Package name: python-librcsb-core-wrapper Version : 1.000 Upstream Author : Vladimir Guranovic * URL : http://sw-tools.rcsb.org/apps/CORE-WRAPPER/index.html * License : RCSB PDB SOFTWARE LICENSE AGREEMENT, Henry Spencer's regex license Programming Lang: C++ Description : library that exports C++ mmCIF accessors to Python This package provides RCSB Core Wrapper, a library that exports C++ mmCIF accessors to Python. . This library is built on top of RCSB CIFPARSE-OBJ, a library that provides an object-oriented interface to information in mmCIF format. -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) iQIcBAEBAgAGBQJQI+EgAAoJEJvS1kCaDFL6PTYP+QHjI4Uuhn1MzAGCuFEaEnBm lufhWz/ulfHXpl0Z/oH7w/zPoE+oXGAFY7Cl5nAVvGGR1FqIdWwT5Rc3TGb+XU2b 4KhR4+Q9WjcLddX/x9NjUF3vM9fBk7dULFmYCyvCdVWsvESV1lh5l/GTNDaAJTIM 7zjnBIOMY9DVnUiWf4pibCNMGA7kBcqhDW+ohljcHK1W8FOQTQTWzgeWgNj7V8i+ 7yjnj9kHKj89TUgkcPtnazibhMYI2TZJuCMUsiZiHuGz7mHT22/ni3KdA5qVzb9k K+edy/HxkCz8B8iqPKjFtY1P/r/FNID68GEy05iRQ1O9fZpq3ABQza/EYqryfXxb vWV0S5ojcXD/b8Dy/jTuTI3kD1yS1aXaiVf7FzIdkYFMZCIhLuNGcmPUSJ4z2yel qEKYbytd+O+ttgGarhdQPR7Z9SXywMMU2mlo090ByPrJ5SVphijfyt/Pjv+5WzI2 /Bh6+XobVOH8qgz8mXCwvpqKfRW8bUhO4GGF3oO7bZTJDlhM/ooaPPybEpU8MTDX FHsrfLwqud74vST6apJNa6m1s6YUY/tqZbbFH60CEjAmkRhszSmlaXDZFr7zSEDz B0atqqBldIvSqQNfaWjcNdEHkZq6U+Fmjb52NCBOnBRVOd84rOQM6O45bVlA2sMB XdfmofkA8OxP7tA6tIYl =pxBx -END PGP SIGNATURE- -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120809161116.28467.97898.reportbug@debian-unstable.rostclust
Bug#680539: ITP: hmmer2 -- profile hidden Markov models for protein sequence analysis (version 2)
Hello Joachim! I use predictprotein (ITP, soon in Debian) and snap (non-free) with version 2 of hmmer. predictprotein is an umbrella package that runs a bunch of bioinformatics tools, none of which are about speech recognition though. snap is for the prediction of effects of non-synonymous mutations in DNA. HMMER is used to find homologues for protein sequences. I am not familiar with speech recognition at all... I have not heard of hmmer being used for it. Best regards, Laszlo On 06/07/12 19:43, Joachim Wiedorn wrote: > Hello, > > Laszlo Kajan wrote on 2012-07-06 18:47: > >> HMMER is an implementation of profile hidden Markov model methods for >> sensitive searches of biological sequence databases using multiple sequence >> alignments as queries. > > Which software/packages do you use together with this package? > > Is there a way to use this package directly together with some speech > recognition software: cmusphinx or simon/julius? > > --- > Have a nice day. > > Joachim (Germany) > -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/4ff72875.7040...@rostlab.org
Bug#680539: ITP: hmmer2 -- profile hidden Markov models for protein sequence analysis (version 2)
Package: wnpp Severity: wishlist Owner: Laszlo Kajan -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 * Package name: hmmer2 Version : 2.3.2 Upstream Author : Sean Eddy * URL : ftp://selab.janelia.org/pub/software/hmmer/ * License : GPL-2+ Programming Lang: C Description : profile hidden Markov models for protein sequence analysis (version 2) HMMER is an implementation of profile hidden Markov model methods for sensitive searches of biological sequence databases using multiple sequence alignments as queries. . Given a multiple sequence alignment as input, HMMER builds a statistical model called a "hidden Markov model" which can then be used as a query into a sequence database to find (and/or align) additional homologues of the sequence family. -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) iQIcBAEBAgAGBQJP9xa1AAoJEJvS1kCaDFL6PPUP/2wv/UE5wlNQ2tYLlRxR7uOO eQ0im3kI1OGHg9BSnhJ6QUMrHJE/O5sRNOL/lvY7AuaRsVyxXXq1+jdCH3YrME92 vh3jSX7/cX2f0Hq/cSWI6Vq60H7MlShP6kNaSrEnMcpRDKUaaeKhR4/CHuzSYMoM dctuImUHKkP8gjBTa8OXX4Y+AaPihOrfBIdcLUhQ9gCRUxi2GdGZU4kbO+KgL1Hm jC9bAlTXwY4kKGCHOYlMN6VV5WK6M6fXjhP/gHCYJ4+zNx4s5nETUTbTkBSPsMw2 Ct3UHhCNm6VgskLrBHI9/TdQnfRE+rX9KZ2r5LORu2xNlFsIxxGKAOKMc90fRRu4 Ms/KsBznt96GOlcGQgb0WwnMZuVYk9LvOHadSPMglZlbQkMopwiS969hdykuoWaT NtSosLQG5wra0feGi1FGEVA2dOx13KlgjeUxQ3NDiWFbRGqtcuXerLVfEwou69gq NJ2adWRoV2O3KTQo1u00GXfBhtlmKxkJJsBn4LtdfYfjaJNY+83SUsjXs8A1HVSt Keer95A3aOCh4djwCu+l1t8u6nSXFniuwsmIWgx+0zN/74r4VJRSeHRG9eJxczkw N2hM18j/7PJzfgQUx2tqacYsxS4aUcqK9xaaw2CBHtDTG3tvmAHTJJod9MclslhM SnteNltP14xthG1DyneD =QOd2 -END PGP SIGNATURE- -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120706164754.26280.39267.reportbug@debian-unstable.rostclust
Bug#676384: ITP: libsort-key-top-perl -- select and sort top n elements
Package: wnpp Severity: wishlist Owner: Laszlo Kajan * Package name: libsort-key-top-perl Version : 0.06 Upstream Author : Salvador Fandiño * URL : http://search.cpan.org/~salva/Sort-Key-Top-0.06/lib/Sort/Key/Top.pm * License : Perl Artistic Programming Lang: Perl Description : select and sort top n elements in Perl The functions available from this module select the top n elements from a list using several common orderings and custom key extraction procedures. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120606160231.26668.79895.reportbug@n0d.rostclust
Bug#669259: ITP: dssp -- protein secondary structure assignment based on 3D structure
Package: wnpp Severity: wishlist Owner: Laszlo Kajan * Package name: dssp Version : 2.0.4 Upstream Author : Maarten L. Hekkelman * URL : http://www.cmbi.ru.nl/dssp/ * License : Boost-1.0 Programming Lang: C++ Description : protein secondary structure assignment based on 3D structure DSSP is an application to assign the secondary structure of a protein based on its three dimensional (3D) structure. . This version (2) of DSSP is a rewrite that produces the same output as the original DSSP, but deals better with exceptions in PDB files and is much faster. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120418135850.3869.8805.reportbug@debian-unstable.rostclust
Bug#666194: ITP: librg-blast-parser-perl -- very fast NCBI BLAST parser - binding for perl
Package: wnpp Severity: wishlist Owner: Laszlo Kajan * Package name: librg-blast-parser-perl Version : 0.02 Upstream Author : Laszlo Kajan * URL : http://rostlab.org/ * License : Artistic Programming Lang: Perl Description : very fast NCBI BLAST parser - binding for perl This package contains perl binding for a very fast C/C++ library for NCBI BLAST -m 0 (default) output parsing. BLAST results are returned in a convenient hash structure. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120329154711.4428.73210.reportbug@debian-unstable.rostclust
Bug#666193: ITP: librostlab-blast -- very fast C++ library for parsing NCBI BLAST output
Package: wnpp Severity: wishlist Owner: Laszlo Kajan * Package name: librostlab-blast Version : 1.0.0 Upstream Author : Laszlo Kajan * URL : http://rostlab.org/ * License : LGPL Programming Lang: C, C++ Description : very fast C++ library for parsing NCBI BLAST output This package provides a very fast library for parsing the NCBI BLAST default (-m 0) output. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120329154627.4377.87212.reportbug@debian-unstable.rostclust
Bug#666192: ITP: librostlab -- C++ library from the Rost Lab
Package: wnpp Severity: wishlist Owner: Laszlo Kajan * Package name: librostlab Version : 1.0.20 Upstream Author : Laszlo Kajan * URL : http://rostlab.org/ * License : LGPL-3+ Programming Lang: C++ Description : C++ library from the Rost Lab The library provides the following facilities: * current working directory resource * exception with stack backtrace * file lock resource * passwd and group structures for C++ * effective uid and gid resource * rostlab::bio::seq class with stream input operator for FASTA format * umask resource -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120329153955.4331.70988.reportbug@debian-unstable.rostclust
Bug#661111: ITP: ffindex -- simple index/database for huge amounts of small files
Package: wnpp Severity: wishlist Owner: Laszlo Kajan * Package name: ffindex Version : 0.9.3 Upstream Author : Andreas Hauser * URL : http://pubshare.genzentrum.lmu.de/scientific_computing/software/ffindex/ * License : CC-BY-SA-3.0 Programming Lang: C Description : simple index/database for huge amounts of small files FFindex is a very simple index/database for huge amounts of small files. The files are stored concatenated in one big data file, separated by '\0'. A second file contains a plain text index, giving name, offset and length of the small files. The lookup is currently done with a binary search on an array made from the index file. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120224092231.9440.34981.reportbug@debian-unstable.rostclust
Bug#660272: ITP: sift -- predict if an amino acid substitution in a protein has phenotypic effect
Package: wnpp Severity: wishlist Owner: Laszlo Kajan * Package name: sift Version : 3.0 Upstream Author : Pauline Ng * URL : http://sift-dna.org/ * License : FHCRC NONCOMMERCIAL LICENSE <ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blimps/LICENSE> Programming Lang: C Description : predict if an amino acid substitution in a protein has phenotypic effect SIFT is a sequence homology-based tool that sorts intolerant from tolerant amino acid substitutions and predicts whether an amino acid substitution in a protein will have a phenotypic effect. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120217213006.3154.76869.reportbug@debian-unstable.rostclust
Bug#659964: ITP: proftmb -- per-residue prediction of bacterial transmembrane beta barrels
Package: wnpp Severity: wishlist Owner: Laszlo Kajan * Package name: proftmb Version : 1.1.7 Upstream Author : Henry Bigelow * URL : http://rostlab.org/ * License : GPL Programming Lang: C++ Description : per-residue prediction of bacterial transmembrane beta barrels proftmb provides a four state (up-strand, down-strand, periplasmic loop, and outer loop) per-residue prediction for the protein. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120215112659.1320.23888.reportbug@debian-unstable.rostclust
Bug#657897: ITP: blimps -- FHCRC BLocks IMProved Searcher
Package: wnpp Severity: wishlist Owner: Laszlo Kajan * Package name: blimps Version : 3.9 Upstream Author : Jorja Henikoff * URL : ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blimps/ * License : FHCRC NONCOMMERCIAL LICENSE <ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blimps/LICENSE> Programming Lang: C Description : blocks database improved searcher BLIMPS (BLocks IMProved Searcher) is a searching tool that scores a sequence against blocks or a block against sequences. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120129173819.11090.15839.report...@rostlab.informatik.tu-muenchen.de
Bug#656626: ITP: hhsuite -- sensitive protein sequence searching based on HMM-HMM alignment
Package: wnpp Severity: wishlist Owner: Laszlo Kajan * Package name: hhsuite Version : 2.0.4 Upstream Author : Johannes Soeding, Michael Remmert, Andreas Hauser , Andreas Biegert * URL : http://toolkit.genzentrum.lmu.de/sections/search * License : GPLv3 Programming Lang: C++ Description : sensitive protein sequence searching based on HMM-HMM alignment The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). It contains HHsearch and HHblits among other programs and utilities. . HHsearch takes as input a multiple sequence alignment (MSA) or profile HMM and searches a database of HMMs (e.g. PDB, Pfam, or InterPro) for homologous proteins. HHsearch is often used for protein structure prediction to detect homologous templates and to build highly accurate query-template pairwise alignments for homology modeling. . HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and, using an iterative search strategy, adds significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120120143227.13631.99357.reportbug@debian-unstable.rostclust
Bug#655336: ITP: reprof -- protein secondary structure and accessibility predictor
Package: wnpp Severity: wishlist Owner: Laszlo Kajan * Package name: reprof Version : 1.0.0 Upstream Author : Peter Hoenigschmid * URL : http://rostlab.org/ * License : GPL Programming Lang: Perl Description : protein secondary structure and accessibility predictor 'reprof' is an improved implementation of 'prof', a popular protein secondary structure and accessibility predictor. Prediction is either done from protein sequence alone or from an alignment - the latter should be used for optimal performance. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120110133020.32349.44160.reportbug@n0d.rostclust
Bug#649995: ITP: libai-fann-perl -- Perl wrapper for the FANN library
Package: wnpp Severity: wishlist Owner: Laszlo Kajan * Package name: libai-fann-perl Version : 0.10 Upstream Author : Salvador Fandino * URL : http://fann.sf.net/ * License : Perl Artistic License Programming Lang: C, C++, Perl Description : Perl wrapper for the FANN library This module provides a Perl wrapper for the FANN library (http://fann.sf.net). -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/2025113953.12840.59231.reportbug@n0d.rostclust
Bug#643669: ITP: pp-popularity-contest -- PredictProtein popularity contest
Package: wnpp Severity: wishlist Owner: Laszlo Kajan * Package name: pp-popularity-contest Version : 1.0.3 Upstream Author : Laszlo Kajan * URL : http://www.rostlab.org/ * License : GPL Programming Lang: C++ Description : PredictProtein popularity contest The pp-popularity-contest package sets up a cron job that periodically submits the developers anonymous statistics on the usage of Rost Lab prediction methods installed on this system. . This information helps to make decisions like which packages should receive high priority when fixing bugs or receive funding for further development and support. This information is also very important when the Rost Lab applies for funding. . Without the funding received based on the usage statistics you contribute by installing this package none of the packages on Debian could have been made available to you at no cost. . Please install this package when it is recommended. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110928143811.2433.28670.reportbug@n0d.rostclust
Bug#643630: ITP: librg-utils-perl -- parsers and format conversion utilities used by (e.g.) profphd
Package: wnpp Severity: wishlist Owner: Laszlo Kajan * Package name: librg-utils-perl Version : 1.0.41 Upstream Author : Burkhard Rost * URL : http://www.rostlab.org/ * License : GPL Programming Lang: Perl Description : parsers and format conversion utilities used by (e.g.) profphd This package contains tools like: * blast2saf.pl, blastpgp_to_saf.pl, conv_hssp2saf.pl, copf.pl, hssp_filter.pl, safFilterRed.pl and modules like: * RG:Utils::Conv_hssp2saf RG:Utils::Copf RG:Utils::Hssp_filter -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110928084729.27937.48522.reportbug@n0d.rostclust
Bug#643323: ITP: profphd-utils -- profphd helper utilities convert_seq and filter_hssp
Package: wnpp Severity: wishlist Owner: Laszlo Kajan * Package name: profphd-utils Version : 1.0.7 Upstream Author : Laszlo Kajan * URL : http://rostlab.org/ * License : GPL Programming Lang: Fortran Description : profphd helper utilities convert_seq and filter_hssp The package provides the following binary utilities: convert_seq, filter_hssp. These are used by prof from the profphd package: a secondary structure, accessibility and transmembrane helix predictor from Burkhard Rost. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110927091028.23047.72131.reportbug@n0d.rostclust
Bug#643324: ITP: profphd -- secondary structure and solvent accessibility predictor
Package: wnpp Severity: wishlist Owner: Laszlo Kajan * Package name: profphd Version : 1.0.35 Upstream Author : Laszlo Kajan * URL : http://rostlab.org/ * License : GPL Programming Lang: Perl Description : secondary structure and solvent accessibility predictor Solvent accessibility is predicted by a neural network method rating at a correlation coefficient (correlation between experimentally observed and predicted relative solvent accessibility) of 0.54 cross-validated on a set of 238 globular proteins (Rost & Sander, Proteins, 1994, 20, 216-226; evaluation of accuracy). The output of the neural network codes for 10 states of relative accessibility. Expressed in units of the difference between prediction by homology modelling (best method) and prediction at random (worst method), PROFacc is some 26 percentage points superior to a comparable neural network using three output states (buried, intermediate, exposed) and using no information from multiple alignments. . Transmembrane helices in integral membrane proteins are predicted by a system of neural networks. The shortcoming of the network system is that often too long helices are predicted. These are cut by an empirical filter. The final prediction (Rost et al., Protein Science, 1995, 4, 521-533; evaluation of accuracy) has an expected per-residue accuracy of about 95%. The number of false positives, i.e., transmembrane helices predicted in globular proteins, is about 2%. . The neural network prediction of transmembrane helices (PHDhtm) is refined by a dynamic programming-like algorithm. This method resulted in correct predictions of all transmembrane helices for 89% of the 131 proteins used in a cross-validation test; more than 98% of the transmembrane helices were correctly predicted. The output of this method is used to predict topology, i.e., the orientation of the N-term with respect to the membrane. The expected accuracy of the topology prediction is > 86%. Prediction accuracy is higher than average for eukaryotic proteins and lower than average for prokaryotes. PHDtopology is more accurate than all other methods tested on identical data sets. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110927092444.23496.83860.reportbug@n0d.rostclust
Bug#641799: ITP: libzerg-perl -- fast perl module for parsing the output of NCBI BLAST programs
Package: wnpp Severity: wishlist Owner: Laszlo Kajan * Package name: libzerg-perl Version : 1.0.4 Upstream Author : Apuã Paquola * URL : http://code.google.com/p/libzerg/ * License : GPL Programming Lang: Perl Description : fast perl module for parsing the output of NCBI BLAST programs The Zerg library contains a C/flex lexical scanner for BLAST reports and a set of supporting functions. It is centered on a "get_token" function that scans the input for specified lexical elements and, when one is found, returns its code and value to the user. . It is intended to be fast: for that we used flex, which provides simple regular expression matching and input buffering in the generated C scanner. And it is intended to be simple in the sense of providing just a lexical scanner, with no features whose support could slow down its main function. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110916101403.15746.40076.reportbug@n0d.rostclust
Bug#641581: ITP: libzerg -- C library for parsing the output of NCBI BLAST programs
Package: wnpp Severity: wishlist Owner: Laszlo Kajan * Package name: libzerg Version : 1.0.7 Upstream Author : Apua C.M. Paquola * URL : http://code.google.com/p/libzerg/ * License : GNU GPL v2 Programming Lang: C Description : C library for parsing the output of NCBI BLAST programs Reference : Paquola, Apuã C M, Machado, Abimael A, Reis, Eduardo M, Da Silva, Aline M, and Verjovski-Almeida, Sergio: Zerg: a very fast BLAST parser library., Bioinformatics 19(8), volume 19, 1035–6, May 2003 Zerg is a C library for parsing the output of NCBI BLAST programs. Based on a GNU Flex-generated lexical scanner, it runs extremely fast, being especially useful for processing large volumes of data. Benchmark tests show that Zerg is over two orders of magnitude faster than some widely used BLAST parsers. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110914132043.32423.19399.reportbug@n0d.rostclust
