[Bio-software] Re: Pairwise alignements versus multiple alignement for distance matrix

Kevin Karplus via bio-soft%40net.bio.net (by karplus from cheep.cse.ucsc.edu)
Wed Feb 28 08:45:00 EST 2007

On 2007-02-28, Ahmed Moustafa <ahmed from pobox.com> wrote:
> But MSA methods perform the pairwise alignments anyway as an initial 
> step to cluster or join the sequences in the multiple alignment. Also 
> MSA methods are approximation while pairwise alignment methods computes 
> the optimal alignments, so they give absolute values representing the 
> relatednesses (or distances) between the sequences.

Only very slow (and ancient) MSA methods start with full pairwise alignments.

Multiple sequence alignments are better alignments than independent
pairwise ones, because they can better disambiguate alignments where
the signal is weak.  The evolutionary distance measures from MSAs are
crude, but the ones from pairwise alignments alignments are often even

Kevin Karplus 	karplus from soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
(Senior member, IEEE)	(Board of Directors & Chair of Education Committee, ISCB)
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