transdecoder_2.0.1+dfsg-2_all.deb


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Description

transdecoder - find coding regions within RNA transcript sequences

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.

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    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

    • /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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