scoring matrix of blast

Question

[sharma_tina189059]

hi,

can anyone tell me about calculating raw value in blast. I know the formula that it is the sum of all match, mismatch and gaps and used to calculate the bit score. but based on scoring matrix how can we calculate two amino acid sequence. I need to resemble my results with the results of blast.

Answer 1

[wpwupingwp]

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins

In Algorithm parameters, choose your matrix