[ssml] Pairwise sequence alignment

[Kevin Karplus]

Rajesh asked "What is the best program (to run locally) for pairwise
comparison of protein sequences (like bl2seq[blast], water & needle
[EMBOSS] )?"

There is no "best" program for this purpose.  Simple pairwise
alignment has been implemented many times and the implementations are
mostly equivalent, as the algorithm is quite simple.  If you have to
do many large alignments, you might want one of the implementations
that is space-efficient.  This tends to matter more for DNA aligners
than protein aligners, and most protein sequences are relatively short.

If you plan later to do something other than pairwise alignment (such
as multiple alignments, profile-sequence alignment, or profile-profile
alignment), you will probably find that the tool you use for that
purpose can do a perfectly adequate job of pairwise alignment also.
So the best tool is the one that generalizes in the direction you want
to go.

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Kevin Karplus 	karplus at 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, ISCB)
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck (lapsed)
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