[ssml] Re: pdb-l: All-vs-All Global protein seq alignment score

Kevin Karplus karplus at soe.ucsc.edu
Mon Jan 10 15:31:33 EST 2005

I rarely have a need for global alignment (unless the proteins have
been pre-trimmed to have matching domains, global alignment is usually
over alignment), and I rarely have a need for all-vs-all alignment of
single sequences (I get much better alignments by doing iterative

If you are sure that you are working on the right problem, there are
plenty of global aligners available.  Almost all the standard tool
suites include one.  http://www.hku.hk/bruhk/sgaln.html contains a
list of a few of the more common ones (found by googling 
	global alignment
, a task that I thought anyone who could send e-mail to these mailing
lists was capable of).

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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