SYNOPSIS

blt find-orfs start-potition < file.seq
blt fasta2seq < file.fasta | blt find-orfs offset

DESCRIPTION

blt find-orfs locates start and stop codon sequences within a raw DNA or RNA sequence.

Currently, it reports the location of a start codon and the next stop codon. Hence, if a second start codon occurs within an ORF, or a stop codon occurs between ORFS, they will not be reported. These codons may be found by specifiying an appropriate start position.

Options to search only for only start codons or only stop codons may be added in the future.

The offset argument is 0-based and indicates an offset from the current position in the input stream. I.e. use 0 to start a the beginning of the file.

EXAMPLES

blt fasta2seq < file.dasta | blt find-orfs 1

SEE ALSO

blt(1), blt-fasta2tsv(1)

AUTHOR

J. Bacon