HTS protein to protein aligner or DNA to Protein aligner

Question

[swttalyan]

Hi, I would like to align short DNA/Protein reads on a reference protein database, But would like to change the scoring matrix from BLOSUM or any with some amino acid propensity values (Distance Matrix) and would also like to put some alignment threshold like minimum number of match, mismatch for a defined read length. Could somebody know any aligner which can do the same for me or know any aligner which I can change some how to do this type of alignment.

Thanking you in advance.

Best Sweta

Answer 1

[Asaf]

The only aligners I know that allow you to change the substitution matrix are in EMBOSS: needle, water, supermatcher and I think there's another one for fast global alignment. It won't be too efficient though.

[GenoMax]

Blast will allow matrix specification but we don't know how long the input sequences are that OP is working with, so that may not be an option.