1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
|
Source: transdecoder
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Michael R. Crusoe <crusoe@debian.org>,
Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
liburi-perl,
ncbi-blast+ <!nocheck>,
hmmer <!nocheck>,
r-base-core <!nocheck>,
r-cran-ggplot2 <!nocheck>,
r-bioc-seqlogo <!nocheck>
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/transdecoder
Vcs-Git: https://salsa.debian.org/med-team/transdecoder.git
Homepage: https://transdecoder.github.io/
Rules-Requires-Root: no
Package: transdecoder
Architecture: all
Depends: ${misc:Depends},
${perl:Depends},
liburi-perl,
r-base-core,
python3
Recommends: r-cran-ggplot2,
r-bioc-seqlogo,
hmmer
Suggests: transdecoder-doc
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.
|
