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// Are there any function that can calculate score for the aligned sequences give parameters?
// April 16, 2011 at 7:39 AM

http://stackoverflow.com/questions/5686211/are-there-any-function-that-can-calculate-score-for-the-aligned-sequences-give-pa
I try to score the already-aligned sequences.
Let say

seq1 = 'PAVKDLGAEG-ASDKGT--SHVVY----------TI-QLASTFE'
seq2 = 'PAVEDLGATG-ANDKGT--LYNIYARNTEGHPRSTV-QLGSTFE'


with given parameters

substitution matrix : blogsum62
gap open penalty : -5
gap extension penalty : -1


I did look through the biopython cookbook but all i can get is substitution matrix blogsum62 but I feel that it must have someone already implemented this kind of library.

So can anyone suggest any libraries or shortest code that can solve my problem?

Thx in advance


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