{"bugs":[],"categories":[{"categoryid":353,"name":"sci-biology","summary":"The sci-biology category contains software that can be used in biological and related scientific environments."}],"changelog":[{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"0b7a976d47e5596c1b85aea1334c4b5c77d61c49","committime":"2024-09-23T15:03:57","packageid":51727,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"fkobi@pm.me","authorname":"Filip Kobierski","body":"Signed-off-by: Filip Kobierski \nCloses: https:\/\/github.com\/gentoo\/gentoo\/pull\/37844\nSigned-off-by: Andrew Ammerlaan ","commitid":"c57e8e68f3470545dfcf294030b17cd1ee50c9aa","committime":"2024-07-31T10:33:01","packageid":51727,"repoid":1,"summary":"sci-biology\/sim4: fix pkgcheck issues"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"584e00af3dff9107646129ec7e221dcd741e476d","committime":"2019-10-05T13:06:02","packageid":51727,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"mgorny@gentoo.org","authorname":"Michał Górny","body":"Replace 'mirror:\/\/gentoo\/X -> Y' with plain 'mirror:\/\/gentoo\/Y'. Since\nactual filenames are used on the mirrors, the latter is valid for all\npackages already.\n\nSigned-off-by: Michał Górny ","commitid":"8a7b48a6603365a2fc0d84a2d02d00789ded7134","committime":"2019-10-05T12:26:30","packageid":51727,"repoid":1,"summary":"*\/*: Remove mirror:\/\/gentoo rename hack"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"cbc193907cd2c282b9a09cb481652f7506645800","committime":"2019-08-17T11:46:11","packageid":51727,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-2.3.71, Repoman-2.3.17\nSigned-off-by: David Seifert ","commitid":"4910baea1319791ff5c0ba23a879f757d4d1169b","committime":"2019-08-17T11:19:13","packageid":51727,"repoid":1,"summary":"sci-biology\/sim4: [QA] Version the distfile"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"25093d6359f778b8d1052f66ba9e26fc29ded21a","committime":"2017-02-28T20:35:29","packageid":51727,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"robbat2@gentoo.org","authorname":"Robin H. Johnson","body":"Signed-off-by: Robin H. Johnson ","commitid":"61b861acd7b49083dab687e133f30f3331cb7480","committime":"2017-02-28T19:47:27","packageid":51727,"repoid":1,"summary":"Drop $Id$ per council decision in bug #611234."},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"aa9317696e6e928ae88775a37371f77514699d03","committime":"2017-02-25T20:43:58","packageid":51727,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-2.3.3, Repoman-2.3.1","commitid":"03ccb71c85392ce397e10386bac30b8378f036e5","committime":"2017-02-25T20:31:11","packageid":51727,"repoid":1,"summary":"sci-biology\/sim4: Remove old"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-2.3.3, Repoman-2.3.1","commitid":"f261f34b716be67fe47b1c5c31f1743fbdc9048e","committime":"2017-02-25T20:30:10","packageid":51727,"repoid":1,"summary":"sci-biology\/sim4: Modernise to EAPI 6"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"945f0d2a26da4f944fd06ad6a874f69d37ce1e06","committime":"2015-08-09T09:26:46","packageid":51727,"repoid":1,"summary":"2015-08-09 09:26:21 UTC"},{"authoremail":"robbat2@gentoo.org","authorname":"Robin H. Johnson","body":"This commit represents a new era for Gentoo:\nStoring the gentoo-x86 tree in Git, as converted from CVS.\n\nThis commit is the start of the NEW history.\nAny historical data is intended to be grafted onto this point.\n\nCreation process:\n1. Take final CVS checkout snapshot\n2. Remove ALL ChangeLog* files\n3. Transform all Manifests to thin\n4. Remove empty Manifests\n5. Convert all stale $Header$\/$Id$ CVS keywords to non-expanded Git $Id$\n5.1. Do not touch files with -kb\/-ko keyword flags.\n\nSigned-off-by: Robin H. Johnson \nX-Thanks: Alec Warner - did the GSoC 2006 migration tests\nX-Thanks: Robin H. Johnson - infra guy, herding this project\nX-Thanks: Nguyen Thai Ngoc Duy - Former Gentoo developer, wrote Git features for the migration\nX-Thanks: Brian Harring - wrote much python to improve cvs2svn\nX-Thanks: Rich Freeman - validation scripts\nX-Thanks: Patrick Lauer - Gentoo dev, running new 2014 work in migration\nX-Thanks: Michał Górny - scripts, QA, nagging\nX-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed","commitid":"56bd759df1d0c750a065b8c845e93d5dfa6b549d","committime":"2015-08-08T20:49:04","packageid":51727,"repoid":1,"summary":"proj\/gentoo: Initial commit"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"a637bd65b7fef8e2be4e7fc6e9097479372e0e2e","committime":"2015-06-19T16:38:33","packageid":51727,"repoid":1,"summary":"2015-06-19 16:35:30 UTC"}],"dependencies":[],"depending":[],"ebuilds":[{"archs":["~amd64","~ppc","~x86"],"ebuildid":16855,"firstseen":"2017-02-26T14:36:33.693601","license":"GPL-2","moddate":"2026-03-22T20:20:57","packageid":51727,"repoid":1,"slot":"0","uses":[],"version":"20030921-r2"}],"masks":[],"package":{"categoryid":353,"description":"A program to align cDNA and genomic DNA","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"sim4","packageid":51727,"summary":"sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects end matches when the two input sequences overlap at one end (i.e., the start of one sequence overlaps the end of the other).sim4 employs a blast-based technique to first determine the basic matching blocks representing the \"exon cores\". In this first stage, it detects all possible exact matches of W-mers (i.e., DNA words of size W) between the two sequences and extends them to maximal scoring gap-free segments. In the second stage, the exon cores are extended into the adjacent as-yet-unmatched fragments using greedy alignment algorithms, and heuristics are used to favor configurations that conform to the splice-site recognition signals (GT-AG, CT-AC). If necessary, the process is repeated with less stringent parameters on the unmatched fragments."},"rdependencies":[],"repos":[{"branch":"master","lastcommit":"52197549fd3431fa256b8edbafdcd3702dd0e134","name":"gentoo","path":"\/usr\/portage","repoid":1,"upstream":"origin"}],"tracked":false,"urls":["http:\/\/globin.cse.psu.edu\/html\/docs\/sim4.html"],"uses":[]}