URL: https://github.com/TransDecoder/TransDecoder
Proper Citation: TransDecoder (RRID:SCR_017647)
Description: Software tool to identify 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 genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV.
Synonyms: , Find Coding Regions Within Transcripts
Resource Type: data processing software, standalone software, software resource, software application
Keywords: Identify, candidate, coding, region, transcript, sequence, de novo, RNAseq, assembly, alignment, genome, open, reading, frame, homology, protein, bio.tools
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