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


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Description

transdecoder-doc - find coding regions within transcripts

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

Requires

    Download

    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

    • /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

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