About

Translates nucleotides (DNA & RNA) in FASTA format to aminoacid sequences and can handle translation of ambiguous codons using IUPAC ambiguity codes.

Usage

Defaults to translating the first frame in forward direction, doesn't stop on STOP codons, uses * as STOP symbol and X for untranslatable codons.

Can translate sequences from a file or STDIN/PIPE (by passing - as filename) and outputs to STDOUT.

Options

• -q or --quiet: silence warning messages
• -a or --all_frames: output translation for all 6 possible frames
• -f or --frame i: specify which frame to output (0 to 5). Frames 0 to 2 are forward strand, 3 to 5 are reverse strand.
• -s or --first_stop: stop translation when first stop codon is found
• -t or --stop_codon: character to use as stop symbol. Defaults to *
• -n or --no_bogus: skips untranslatable codons instead of printing X

Testing

A small test case is available. Use:

make test

to run it.

Authors

• Luis Pedro Coelho
• Renato Alves

License: GPLv3+

Test status: