Public Domain Programs & Tools, continued

Issues include

• limited vocabulary for DNA: ACGTN and for peptides (20 possible chars)
• substitutions (e.g., A --> C)
• In/Dels (that is, relative insertions/deletions)

Seq lengths from 100 to 10,000,000 bases for DNA
Scoring based on how good each base in an input sequence is (qual score)

For peptides, 3 DNA bases code for one amino acid. So we have 6 frames (start at base 1,2,3 or similar in reverse direction) with the issues of codon mapping as well as in/dels