Protein Sequence - Combinatoric Table

Sonnhammer E./Durbin esr at al.*
Sat Jan 15 12:29:03 EST 1994


"Edwin Wright" writes:

   Does anyone know of any research underway to produce some kind of table or
   universal combinatoric sequence structure for all proteins, in an effort to
   delimit the possible combinations of protein sequences?


Edwin, 

I think you would get more answers if you more explicitly say what you
mean by your question.  Are you referring to the combinatorial nature
of protein domains in mosaic proteins, or something else?  What would
the table you're asking for look like and what do you mean by
"universal combinatoric sequence structure for all proteins"?
   Also, what kind of questions would you like to answer - something
like "given protein domain A, which other domains has it been observed
to be fused to?", or what?

I have been involved in a project where the goal was to cluster a
protein sequence database into families of domains, taking the
combinatorial nature of proteins into account.  If this is any help to
you, you can pick up the resulting clustered database (as multiple
sequence alignments) and a preprint of the paper by anon. FTP at
cele.mrc-lmb.cam.ac.uk in /pub/prodom.

Erik Sonnhammer
Sanger Centre
Cambridge UK



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