Bioperl: Start of alignment debate...

Keith Allen
Thu, 14 Jan 1999 18:00:08 -0800


	I'm not 100% sure I understand what you're getting at
in this requirement (which none of the existing objects support

3) The object should provide an easy way of saying "I have
residue XXX in this protein, what is the aligned residues in
this protein"

but I can definitely see querying the alignment object for things
like "to what extent are the following cysteines conserved" or
"give me the subset of sequences that have/dont have such and
such crucial residue/motif".

OK, so maybe it doesn't need to support a motif search (;-), but
you see what I mean.

				-Keith Allen

Keith Allen, PhD
Bioinformatics Specialist
Deltagen, Inc
1031 Bing St.
San Carlos, CA 94070
650 610-6826

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