Re: Scoring matrixes, negative values for Y==Y?

> Normally, scores range from 0 and up, correct?

No, negative values are possible and they are necessary if you are looking
for local alignments..

> Are there matrixes in use that can have negative values for an exact
> identity match?

Not that I know of.

> Would such a matrix have any use?

A matrix that looks for local alignments of the complementary DNA sequence
could have negative values for exact matches and positive scores for
complementary ones.

Never heard of this tho.

Regards,
Michael.