Comparing alignments of differing length - what's the right test?

Question

[ngarber]

I want to test whether the alignment of a particular short sequence in two proteins is better than the alignment of those whole proteins to each other. What is the right test for this?

What I want to do (in Python):

1. COBALT or BLAST a pre-defined short sequence from Protein A against Protein B
2. COBALT or BLAST the entire Protein A against Protein B
3. Test whether the alignment in (1) is better than the alignment in (2)

I suppose I can just use sequence identity %, but that's not very good - is there a better way?

Answer 1

[lennykovac]

You can compare the scores of the alignments which should indicate the best alignment.

Although I think blast is an overkill for this task. Just use the Needleman-Wunsch(Not my implementation) algorithm for the alignments. There are endless implementations out there and its quite easy to implement it yourself ;D. Then you can compare the scores.