Looking for Identities

Hemang Patel ez017400 at chip.ucdavis.edu
Thu Nov 9 18:48:54 EST 1995


I am looking for a way to take a few proteins and look for common, short 
seuqences that occur in different locations in the primary sequence. This 
is not a question of alignment. Bestfit and pileup only find homologous 
regions if they are contiguous in the overall sequence. Dotplot *seems* 
to do this, but the output is graphical and is sometimes hard to 
interpret and control. 

I do not have a particular sequence I am looking for, I just want the
computer to break the sequences down on its own and search all
possibilities. For example, if a 5 amino acid sequence is in the N-terminal
region of one protein, the C-terminal region of another, and in the middle
of a third protein, how would i find this? Will BLAST do it? Or am I out 
of luck? Thanks


>Hemang Patel	hcpatel at dale.ucdavis.edu

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