An auditory display tool for DNA sequence analysis

The Reading-frame-codons algorithm sonifys each overlapping codon (made up of 3 base) as a single note. Codons in 3 reading frames are sonified using 3 instruments. A start codon is ATG and there are 3 stop codons (TGA, TAG and TAA). These codons act to start or stop protein synthesis. The Protein-sequence algorithm plays only the open reading frame (assume reading frame 1) and non-overlapping codons are mapped to 20 notes, since there are 20 different amino acid residues in a protein. The Tri-nucleotides algorithms plays all codons (64 in total) as individual notes. The two Di-nucleotide algorithms sonify overlapping or non-overlapping motifs of 2 base-pairs. Overlapping motifs are sonified using 2 instruments and only 16 notes are possible. Lastly the Mono-nucleotides algorithm sonifies each individual bases to a single note.

Options only apply to the Reading-frame-codons selection.
With the Silent-until-ATG option, no audio is generated in either frame until an ATG codon is detected, often this causes the sonification to be silent at the begining. The Restart-on-ATG option plays all codons from the beginning of the sequence. For both of these options, a Stop codon will silence the audio in the frame in which it occurs (this effects only one instrument). The Restart-after-10-codons option automatically turns the audio on again in the absence of a Start codon - simply to avoid long periods of silence. Each frames is audible until a STOP codon occurs, ATG restarts the frames audio. The Ignore-Start/Stop option will play all codons for the entire sequence.