sim4 0.0.20121010-1 source package in Ubuntu
Changelog
sim4 (0.0.20121010-1) unstable; urgency=low
* New upstream version
* debian/upstream: add citation information
* debian/source/format: 3.0 (quilt)
* debian/control:
- cme fix dpkg-control
- debhelper 9
- drop cdbs build-depends
- anonscm in Vcs fields
* debian/rules: short dh
* debian/patches/hardening.patch: propagate hardening options
* debian/copyright: DEP5
-- Andreas Tille <email address hidden> Fri, 02 Aug 2013 13:24:50 +0200
Upload details
- Uploaded by:
- Debian Med
- Uploaded to:
- Sid
- Original maintainer:
- Debian Med
- Architectures:
- any
- Section:
- science
- Urgency:
- Low Urgency
See full publishing history Publishing
| Series | Published | Component | Section | |
|---|---|---|---|---|
| Trusty | release | universe | science |
Downloads
| File | Size | SHA-256 Checksum |
|---|---|---|
| sim4_0.0.20121010-1.dsc | 1.3 KiB | 4e10073887fe698a361a7dced7accd1f0b765141016946fd3062d6d2b335f450 |
| sim4_0.0.20121010.orig.tar.gz | 59.8 KiB | d2132f61e47f2de5e35d0b48a0f697ae79ece3e8b91177eae2dfe47bda97b4a5 |
| sim4_0.0.20121010-1.debian.tar.gz | 5.8 KiB | a0f0f9f5ff1cad217463a660f6904902478b1049a33385560d5dc36f26442824 |
Available diffs
No changes file available.
Binary packages built by this source
- sim4: tool for aligning cDNA and genomic DNA
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.
- sim4-dbgsym: debug symbols for package sim4
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.
