Bioperl: Start of alignment debate...

[David J. States]

Actually, blocks style alignments are a case where Ewan's notion of "region 
to region" alignment would be quite useful.  The intervening sequences 
between a pair of blocks are regions that are aligned with each other, it 
is just not clear how eaxactly the residues in this region on one sequence 
are are matched to residues in the corresponding region on another 
sequence.

But this does raise a significant issue.  An alignment is a mapping from 
one sequence to another sequence.  To preserve the use of dynamic 
programming, there is an additional constraint that this mapping preserve 
the linear ordering of residues.  However, this constraint makes it 
impossible to represent some biological relationships such as domaing order 
swaps and domain duplication.  An alignment data structure that makes it 
possible to represent these nonlinear mappings will make it harder to use 
the module in straightforward aligment contexts because you will always 
have to ask is this just a one to one mapping or something funky. 
 Exceptional cases do exist in biology, but 99% of cases don't require the 
exception.  Again, my vote is to keep it simple.

David

----
David J. States, M.D., Ph.D.
Associate Professor and Director
Institute for Biomedical Computing
Washington University in St. Louis
700 S. Euclid Ave.
St. Louis, MO   63110

tel: 314 362 2134
fax: 314 362 0234
email: states@ibc.wustl.edu

-----Original Message-----
From:	Rubin Eitan [SMTP:bcrubin@dapsas1.weizmann.ac.il]
Sent:	Monday, January 25, 1999 2:35 AM
To:	David J. States
Cc:	vsns-bcd-perl@lists.uni-bielefeld.de; 'Ewan Birney'
Subject:	RE: Bioperl: Start of alignment debate...

Just a quick thought - you should consider the blocks type of MSA, i.e.
were some regions are aligned (w/o gaps) and others are simply
disregarded. An alignemnt using blocks would actually be a collection of
alignments, but may still be used as a single alignment for purposes such
as tree construction.

       Eitan.


======================================================================
Eitan Rubin,
Plant Genetics, Weizmann Inst of Science, Rehovot, Israel.
EMail: bcrubin@dapsas1.weizmann.ac.il
Tel: (00972)-(8)9342421 Fax: (00972)-(8)9344181
EitanR@BioMOO (http://bioinfo.weizmann.ac.il/BioMOO) - visit
                                            the GCG help desk

in vivo -> in vitro -> in silico
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