exons & protein domains

Bob Gross bob.gross at dartmouth.edu
Mon Jul 15 10:27:44 EST 1996


Hi again-

I did not receive many responses to my last post on this topic (probably due to
my poor wording of the question), so I thought I'd try again. I would
appreciate hearing the "wisdom" of this group.

My colleagues in Math and Computer Science and I are developing a new grouping
algorithm that allows us to take large numbers of sequences and assign them to
individual groups. All the sequences in each group are related to each other.
What we want to do is take peptide sequences that are translated from single
exons and try to group them.

This would allow us to study the possible relationships among protein domains
that are coded for on individual exons, which might be descendents of the same
primordial exon. Such information might shed some light on evolutionary
processes and might help in understanding the properties of newly sequenced
genes. Ultimately it might provide a database of exons that share common
functions. 

Of course we are aware of databases like the Prosite database that contain many
motifs, but these motifs are usually quite short and probably do not represent
whole functional domains on proteins. Rather, they often represent short
targets, e.g. glycosylation sites, phosphorylation sites, etc. However, there
are some true "domains" such as ATP binding, G-protein GTP binding, DNA
binding, etc. My question to this group is what "domains" would you start off
with in testing the grouping algorithm - based on your biological knowledge?
The three above are starting points. What is of interest are those domains that
are coded for on single exons and that share a common function even thought the
exons might reside on different genes.

Any help would be appreciated. Thanks.

Bob Gross

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