sci-biology / sim4

A program to align cDNA and genomic DNA

Official package sites : http://globin.cse.psu.edu/html/docs/sim4.html ·

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.

v20030921-r2 :: 0 :: gentoo

Modified
License
GPL-2
Keywords
~amd64 ~ppc ~x86
Repository mirror & CI · gentoo
Merge updates from master
Filip Kobierski · gentoo
sci-biology/sim4: fix pkgcheck issues
Signed-off-by: Filip Kobierski <fkobi@pm.me> Closes: https://github.com/gentoo/gentoo/pull/37844 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
Michał Górny · gentoo
*/*: Remove mirror://gentoo rename hack
Replace 'mirror://gentoo/X -> Y' with plain 'mirror://gentoo/Y'. Since actual filenames are used on the mirrors, the latter is valid for all packages already. Signed-off-by: Michał Górny <mgorny@gentoo.org>
Repository mirror & CI · gentoo
Merge updates from master
David Seifert · gentoo
sci-biology/sim4: [QA] Version the distfile
Package-Manager: Portage-2.3.71, Repoman-2.3.17 Signed-off-by: David Seifert <soap@gentoo.org>
Robin H. Johnson · gentoo
Drop $Id$ per council decision in bug #611234.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
David Seifert · gentoo
sci-biology/sim4: Remove old
Package-Manager: Portage-2.3.3, Repoman-2.3.1
David Seifert · gentoo
sci-biology/sim4: Modernise to EAPI 6
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Robin H. Johnson · gentoo
proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed