Source: transdecoder Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Andreas Tille Section: science Priority: optional Build-Depends: debhelper-compat (= 13), liburi-perl Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/transdecoder Vcs-Git: https://salsa.debian.org/med-team/transdecoder.git Homepage: https://transdecoder.github.io/ Rules-Requires-Root: no Package: transdecoder Architecture: all Depends: ${misc:Depends}, ${perl:Depends}, liburi-perl, r-base-core, python3 Suggests: transdecoder-doc Description: 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. Package: transdecoder-doc Architecture: all Multi-Arch: foreign Section: doc Depends: ${misc:Depends}, ${perl:Depends} Description: find coding regions within transcripts 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.