sixpack reads a DNA sequence and writes an output file giving out the forward and reverse sense sequences with the three forward and (optionally) three reverse translations in a pretty display format. A genetic code may be specified for the translation. There are various options to control the appearance of the output file. It also writes a file of protein sequences corresponding to any open reading frames that are larger than the specified minimum size: the default of 1 base shows all possible open reading frames.
The program takes the following steps:
The nucleic acid sequence is read in. The required genetic code is read in from the EGC* data files. The three forward and three reverse translations are created. The name and description are written to the ouput display file. Any required regions to be changed to upper case are changed. Any required regions to be highlighted in HTML colour tags are changed. The reverse sense sequence is placed below the forward sequence. The forward translations are placed above the sequences. The reverse translation are placed below the sequences. The display is written out, split at the ends of lines. Any ORFs that are longer than the specified minimum size are written to the output sequence file.
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An open reading frame is defined in this program as any possible translation between two STOP codons. Optionally, the beginning or end of a sequence may be counted as an ORF even if it's less than the minimal ORF size or (end only) lacking a STOP codon. See the -firstorf and -lastorf options.