[Bioperl-l] What is the gap penalty function for BLOSUM62?

[Yee Man Chan]

Hi,

	I got conflicting usage of gap penalty functions for BLOSUM62
matrix:

ssearch34: g(k) = 7+k
Henikoff & Henikoff paper: g(k) = 8+4*k
Gapped BLAST paper: g(k) = 10+k
Ewan's pSW module: g(k) = 12+2*k

where k is the number of gaps.

	Which one is the correct one? It seems to me all of them use the
exactly the same blosum62 matrix.

Thanks
Yee Man