Hello,
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
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>Hemang Patel hcpatel at dale.ucdavis.edu
