scoring similarities between alignments alignments

Tim Dudgeon dudgeon at britbio.co.uk
Thu Apr 20 10:14:15 EST 1995

Helo software gurus, I hope you can help me with advice on how best to go about
solving a problem.

I need to be able to score the similarities between different protein sequence
alignments. i.e. I have 3 related protein families A, B, C each of which has
any number of members that are readily aligned within the family. I wish to
evaluate the relationships between these families by being able to score
(prefereably tabulate) all the possible comparisons (A vs B, A vs C, B vs C).
All members of each family could be provided as an alignment or I could
generate a profile from it.

Does anyone know of any algorithms that can score the alignment of 2 alignments
or an alignment of 2 profiles, and idealy do this for each set of alignments
and tabulate the results?

Many thanks for your anticipated help.
Pleasse reply by email. I will summarise any useful suggestions and post them
back to this newsgroup if they seem appropriate.


Tim Dudgeon
British Biotech
Phone: 0865 748747
FAX:   0865 717598
email: dudgeon at britbio.co.uk

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