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

[Ewan Birney]

On Thu, 17 Jul 2003, Yee Man Chan wrote:

>
> 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.

the all are; It is user defined. I have always though -12,-2 was the best
combination (as you can see...)



>
> Thanks
> Yee Man
>
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