How To Create Pam Or Blossum Matrix (Substitution Matrix)

Question

[loicatraile]

Hi guys! I´m looking for a hint or if someone has a recipe on how to compute a PAM or BLOSSUM matrix. I found this link: http://www.biorecipes.com/Dayhoff/code.html coded in Darwin but i found out that the code is most probably wrong because i´m unable to recreate the results that are explained there.. i tried in Perl and then in Darwin without success. Any hint would be really appreciated! Thanks!

Answer 1

[Hamish]

The Wikipedia articles are a good place to start:

• Substitution matrix
• Point accepted mutation (PAM)
• BLOSUM

The various papers cited in these articles provide further details about how the matrices are constructed.

As well as PAM and BLOSUM there are various other substitution matrices available, for example:

• Gonnet (PubMed:1604319)
• JTT (PubMed:1633570)
• OPTIMA (PubMed:11056037)
• VTML (PubMed:11752185, PubMed:11382360)

See http://www.genome.jp/aaindex/AAindex/list_of_matrices for a list containing these and more.