Bioperl: Start of alignment debate...

[Keith Allen]

Ewan,

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

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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