Paketti: transdecoder (5.7.1-2)

[ Source: transdecoder  ]

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.

Muut pakettiin transdecoder liittyvät paketit

• dep: liburi-perl

  module to manipulate and access URI strings

• dep: perl

  Larry Wallin kieli tekstitiedostojen analysointia ja raportointia varten

• dep: python3

  interactive high-level object-oriented language (default python3 version)

• dep: r-base-core

  GNU R core of statistical computation and graphics system

• rec: hmmer

  profile hidden Markov models for protein sequence analysis

• rec: r-bioc-seqlogo

  GNU R sequence logos for DNA sequence alignments

• rec: r-cran-ggplot2

  implementation of the Grammar of Graphics

• sug: transdecoder-doc

  find coding regions within transcripts

Imuroi transdecoder

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