transdecoder
find coding regions within RNA transcript sequences
Command lineScience
Not tested on a device yet. What that means
Commands in the package
TransDecoder.LongOrfsTransDecoder.Predict
About transdecoder
From Debian's package description
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.
From Debian's description of the transdecoder package, under that package's license.
Dependencies
Depends on
perlliburi-perlr-base-corepython3
Recommends
r-cran-ggplot2r-bioc-seqlogohmmer
Related apps
- probconsPROBabilistic CONSistency-based multiple sequence alignmentCommand line
- bitseqBayesian Inference of Transcripts from Sequencing DataCommand line
- gffreadGFF/GTF format conversions, region filtering, FASTA sequence extractionCommand line
- salmonwicked-fast transcript quantification from RNA-seq dataCommand line
- rtaxClassification of sequence reads of 16S ribosomal RNA geneCommand line
- repeatmasker-reconfinds repeat families from biological sequencesCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the transdecoder package, under that package's license.
- Description: Debian's description of the transdecoder package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
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