transdecoder-doc_2.0.1+dfsg-2_all.deb


Advertisement

Description

transdecoder-doc - find coding regions within transcripts

Property Value
Distribution Ubuntu 16.04 LTS (Xenial Xerus)
Repository Ubuntu Universe i386
Package name transdecoder-doc
Package version 2.0.1+dfsg
Package release 2
Package architecture all
Package type deb
Installed size 54.72 KB
Download size 15.94 MB
Official Mirror archive.ubuntu.com
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.

Alternatives

Package Version Architecture Repository
transdecoder-doc_2.0.1+dfsg-2_all.deb 2.0.1+dfsg all Ubuntu Universe
transdecoder-doc - - -

Requires

Name Value
perl -

Download

Type URL
Binary Package transdecoder-doc_2.0.1+dfsg-2_all.deb
Source Package transdecoder

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install transdecoder-doc deb package:
    # sudo apt-get install transdecoder-doc

Files

Path
/usr/lib/transdecoder/sample_data/blastp.results.outfmt6
/usr/lib/transdecoder/sample_data/blastp.results.outfmt6.gz
/usr/lib/transdecoder/sample_data/cleanme.pl
/usr/lib/transdecoder/sample_data/pfam.domtblout
/usr/lib/transdecoder/sample_data/pfam.domtblout.gz
/usr/lib/transdecoder/sample_data/runMe.sh
/usr/lib/transdecoder/sample_data/test.genome.fasta
/usr/lib/transdecoder/sample_data/test.genome.fasta.gz
/usr/lib/transdecoder/sample_data/test.tophat.sam
/usr/lib/transdecoder/sample_data/test.tophat.sam.gz
/usr/lib/transdecoder/sample_data/transcripts.bed
/usr/lib/transdecoder/sample_data/transcripts.fasta
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder.bed
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder.cds
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder.genome.bed
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder.genome.gff3
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder.gff3
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder.mRNA
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder.pep
/usr/lib/transdecoder/sample_data/transcripts.gff3
/usr/lib/transdecoder/sample_data/transcripts.gtf
/usr/lib/transdecoder/sample_data/transcripts.gtf.gz
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder_dir/base_freqs.dat
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder_dir/base_freqs.dat.ok
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder_dir/hexamer.scores
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder_dir/hexamer.scores.ok
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder_dir/longest_orfs.cds
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder_dir/longest_orfs.cds.best_candidates.gff3
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores.ok
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder_dir/longest_orfs.cds.scores.selected
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_500_longest.ok
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr80
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder_dir/longest_orfs.cds.top_longest_5000.nr80.clstr
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder_dir/longest_orfs.gff3
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder_dir/longest_orfs.gff3.inx
/usr/lib/transdecoder/sample_data/transcripts.fasta.transdecoder_dir/longest_orfs.pep
/usr/share/doc/transdecoder-doc/README
/usr/share/doc/transdecoder-doc/Release.Notes
/usr/share/doc/transdecoder-doc/changelog.Debian.gz
/usr/share/doc/transdecoder-doc/copyright
/usr/share/doc/transdecoder-doc/run-tests
/usr/share/lintian/overrides/transdecoder-doc

Changelog

See transdecoder_2.0.1+dfsg-2_all.deb changelog.

See Also

Package Description
transdecoder_2.0.1+dfsg-2_all.deb find coding regions within RNA transcript sequences
transfermii-gui_0.6.1-2.1_i386.deb transfer your mii from and to your wiimotes -- GUI
transfermii_0.6.1-2.1_i386.deb transfer your mii from and to your wiimotes
transgui_5.0.1-2_i386.deb Front-end to remotely control Transmission
transifex-client_0.11.1+git15~g655c5e9-1_all.deb Command line interface for Transifex
translate-docformat_0.6-5_all.deb any-to-any document translation system
translate-toolkit_1.13.0-1_all.deb Toolkit assisting in the localization of software
translate_0.6-11_all.deb translates words from English into German or viceversa
transmageddon_1.5-3_all.deb video transcoder for Linux and Unix systems built using GStreamer
transmission-remote-cli_1.7.0-1_all.deb ncurses interface for the Transmission BitTorrent daemon
transmission-remote-gtk_1.1.1-1build1_i386.deb GTK+ interface for the Transmission BitTorrent daemon
transmission_2.84-3ubuntu3_all.deb lightweight BitTorrent client
transrate-tools_1.0.0-1_i386.deb helper for transrate
transtermhp_2.09-2_i386.deb find rho-independent transcription terminators in bacterial genomes
trash-cli_0.12.9.14-2_all.deb command line trashcan utility
Advertisement
Advertisement