In article <329CC8F5.655A at mit.edu>, hdrabkin at mit.edu says...
>Does anyone know of a program that could search the standard sequence
>databases of protein sequences for a particular di or tri peptide
>sequence, restricting the search to just the N-terminal? For example,
>how many proteins begin with V-D, or M-V-D?
Yes, I had that need once when choosing targets for anti-peptide
antibodies at the termini of proteins (they work great! see Biochem.
Pharmacol. 49, 39-47 ). At the time I just clanked through
the SwissProt database using a Turbo BASIC program. This is fairly
trivial to do - the only problem being interpreting the database
sequence format. These days its probably a job for Awk etc.
If no one comes up with any pointers to an existing solution then
let me know which platform you are using and what database(s) you
have access to.
It was a suprise to find how the terminal context of the
tripeptide epitope was such a strong influence on the binding
specificity (I guess the immune system just likes to pick on "ends").
(and a Happy Turkey Day to them that cares)
Bernard Murray, Ph.D.
bernard at elsie.nci.nih.gov (National Cancer Institute, NIH, Bethesda MD, USA)