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Translate BED transcripts (version 0.1.0)
thickStart and thickEnd define protein coding region, blocks define exon regions
BED Filtering Options
BED Filtering Options 0
Translation Options
Translation Options 0
Fasta ID Options
Fasta ID Options 0

Translate transcripts from the input BED file into protein sequences.

The genomic sequence:

  • may be supplied in an extra column in the BED input file
  • retrieved from a twobit genomic reference file
  • retrieved from the Ensembl REST API for Ensembl transcripts


  • BED file with at least the standard 12 columns
  • Genome reference in twobit format (optional)


  • FASTA of transcript translations
  • BED with the genomic location of the translated protein. The added 13th column contains the protein sequence.


  • Feature translation
    • cDNA - three frame translations of the cDNA sequences with an output for each sequence between STOP codons
    • CDS - three frame translations of CDS (coding sequence defined by thickStart and thickEnd in the BED file)
  • Translation filtering
    • can be trimmed to a Methionine start codon
    • can be split into peptides by an enzyme digestion
    • must exceed specified minimum length
  • BED Filtering
    • genomic regions
    • ensembl biotype if the BED contains the 20 columns as retrieved from the Ensembl REST API