Six Frame DNA Translation

From Mswiki

To convert a DNA FASTA database to a protein FASTA database requires a six-frame translation of the DNA sequence. To run, first:

/data/6/jrjohns1/perlscripts/SixFrameTranslate input.fasta

This will create a file called input.fasta.sixframe. You must run the following script to get a useful database:

/data/6/jrjohns1/perlscripts/SixFrame2FASTA 50 input.fasta.sixframe

Where 50 is the minimum number of amino acids within each ORF without incurring a stop codon (user can change), and input.fasta.sixframe is the output from the SixFrameTranslate scripts. The second script will create a file called input.fasta.sixframe_50.fasta