How to use self made BLOSUM matrix in standalone blast?

11 November 2012 1 9K Report

I have my own self made BLOSUM matrix (made for a specific problem which is not being solved by conventional BLOSUM/PAM matrices). I want to use it in standalone BLAST.

Although BLAST has -M option but it takes input as -m [STRING]. That means you can only use predefined MATRICES which are available in BLAST. Can anybody help me on how to solve this problem?

Sandeep Singh

It doesn't work like that. I have tried it. I think these matrices are included in the executable and even after removing all the predefined matrices from "data" directory, BLAST still works. I don't know how to include my matrix in the source code as i am unable to understand how matrix is represented in source code.

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