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Source: transdecoder
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Michael R. Crusoe <michael.crusoe@gmail.com>,
Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
cd-hit,
liburi-perl
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/transdecoder.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/transdecoder.git
Homepage: https://transdecoder.github.io/
Package: transdecoder
Architecture: all
Depends: ${misc:Depends},
${perl:Depends},
cd-hit,
liburi-perl
Description: find coding regions within RNA transcript sequences
TransDecoder identifies candidate coding regions within transcript sequences,
such as those generated by de novo RNA-Seq transcript assembly using Trinity,
or constructed based on RNA-Seq alignments to the genome using Tophat and
Cufflinks.
.
TransDecoder identifies likely coding sequences based on the following
criteria:
* a minimum length open reading frame (ORF) is found in a transcript sequence
* a log-likelihood score similar to what is computed by the GeneID software
is > 0.
* the above coding score is greatest when the ORF is scored in the 1st
reading frame as compared to scores in the other 5 reading frames.
* if a candidate ORF is found fully encapsulated by the coordinates of
another candidate ORF, the longer one is reported. However, a single
transcript can report multiple ORFs (allowing for operons, chimeras, etc).
* optional the putative peptide has a match to a Pfam domain above the noise
cutoff score.
Package: transdecoder-doc
Architecture: all
Multi-Arch: foreign
Section: doc
Depends: ${misc:Depends},
${perl:Depends}
Description: find coding regions within transcripts
TransDecoder identifies candidate coding regions within transcript sequences,
such as those generated by de novo RNA-Seq transcript assembly using Trinity,
or constructed based on RNA-Seq alignments to the genome using Tophat and
Cufflinks.
.
TransDecoder identifies likely coding sequences based on the following
criteria:
* a minimum length open reading frame (ORF) is found in a transcript sequence
* a log-likelihood score similar to what is computed by the GeneID software
is > 0.
* the above coding score is greatest when the ORF is scored in the 1st
reading frame as compared to scores in the other 5 reading frames.
* if a candidate ORF is found fully encapsulated by the coordinates of
another candidate ORF, the longer one is reported. However, a single
transcript can report multiple ORFs (allowing for operons, chimeras, etc).
* optional the putative peptide has a match to a Pfam domain above the noise
cutoff score.
.
This package contains the documentation and sample data.
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