[EMBOSS] Assymetrical Scoring Matrix

[pmr at ebi.ac.uk]

Hi Ryan,

> I have an assymetrical scoring matrix ie the substitution scores from
> organism A to organism B is not the same as from organism B to organism
> A.
>
> How can I be sure that when I'm comparing sequence A to sequence B, that
> stretcher is using the correct side of the diagonal?

Use two test sequences that have one residue repeated for sequence A and
another repeated for sequence B (with a positive score in the matrix) and
check the alignment score to see which was used. Then swap the sequences
and try again.

For example:

stretcher asis::qqqqqqqqqq asis:nnnnnnnnnn

The alignment score will be 10 times the score that was used (as there are
10 residues in each sequence)

Hope that helps ... and this is something we should add to our QA testing.

Peter