transdecoder_2.0.1+dfsg-2_all.deb


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Description

transdecoder - find coding regions within RNA transcript sequences

Property Value
Distribution Ubuntu 16.04 LTS (Xenial Xerus)
Repository Ubuntu Universe i386
Package name transdecoder
Package version 2.0.1+dfsg
Package release 2
Package architecture all
Package type deb
Installed size 274 B
Download size 55.71 KB
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.

Alternatives

Package Version Architecture Repository
transdecoder_2.0.1+dfsg-2_all.deb 2.0.1+dfsg all Ubuntu Universe
transdecoder - - -

Requires

Name Value
cd-hit -
liburi-perl -
perl -

Download

Type URL
Binary Package transdecoder_2.0.1+dfsg-2_all.deb
Source Package transdecoder

Install Howto

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

Files

Path
/usr/bin/TransDecoder.LongOrfs
/usr/bin/TransDecoder.Predict
/usr/lib/transdecoder/TransDecoder.LongOrfs
/usr/lib/transdecoder/TransDecoder.Predict
/usr/lib/transdecoder/PerlLib/Fasta_reader.pm
/usr/lib/transdecoder/PerlLib/GFF3_utils.pm
/usr/lib/transdecoder/PerlLib/Gene_obj.pm
/usr/lib/transdecoder/PerlLib/Gene_obj_indexer.pm
/usr/lib/transdecoder/PerlLib/Longest_orf.pm
/usr/lib/transdecoder/PerlLib/Nuc_translator.pm
/usr/lib/transdecoder/PerlLib/TiedHash.pm
/usr/lib/transdecoder/util/cdna_alignment_orf_to_genome_orf.pl
/usr/lib/transdecoder/util/compute_base_probs.pl
/usr/lib/transdecoder/util/cufflinks_gtf_genome_to_cdna_fasta.pl
/usr/lib/transdecoder/util/cufflinks_gtf_to_alignment_gff3.pl
/usr/lib/transdecoder/util/cufflinks_gtf_to_bed.pl
/usr/lib/transdecoder/util/ffindex_resume.pl
/usr/lib/transdecoder/util/gene_list_to_gff.pl
/usr/lib/transdecoder/util/get_top_longest_fasta_entries.pl
/usr/lib/transdecoder/util/gff3_file_to_bed.pl
/usr/lib/transdecoder/util/gff3_file_to_proteins.pl
/usr/lib/transdecoder/util/index_gff3_files_by_isoform.pl
/usr/lib/transdecoder/util/nr_ORFs_gff3.pl
/usr/lib/transdecoder/util/pfam_mpi.pbs
/usr/lib/transdecoder/util/pfam_runner.pl
/usr/lib/transdecoder/util/remove_eclipsed_ORFs.pl
/usr/lib/transdecoder/util/score_CDS_liklihood_all_6_frames.pl
/usr/lib/transdecoder/util/seq_n_baseprobs_to_logliklihood_vals.pl
/usr/lib/transdecoder/util/bin/.hidden
/usr/share/doc/transdecoder/changelog.Debian.gz
/usr/share/doc/transdecoder/copyright
/usr/share/man/man1/TransDecoder.LongOrfs.1.gz
/usr/share/man/man1/TransDecoder.Predict.1.gz

Changelog

2015-12-28 - Andreas Tille <tille@debian.org>
transdecoder (2.0.1+dfsg-2) unstable; urgency=medium
[ Andreas Tille ]
* Slightly enhanced short description
* Lintian override for false positive package-contains-timestamped-gzip
* DEP3 headers
[ Charles Plessy ]
* Make output reproducible.
Closes: #809187

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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
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transrate-tools_1.0.0-1_i386.deb helper for transrate
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