Multiple alignment of protein sequences

Bill Pearson wrp at cyclops.micr.Virginia.EDU
Thu Feb 6 13:29:40 EST 1992

	If you have access to a UNIX machine, you should consider the MSA
program, which should be available from Stephen Altschul at the NCBI/NLM.

	%A D. J. Lipman
	%A S. F. Altschul
	%A J. D. Kececioglu
	%T A tool for multiple sequence alignment
	%J Proc. Natl. Acad. Sci. USA
	%D 1989
	%V 86
	%N 12
	%P 4412-5

This program works well for up to about 5 sequences of 200 residues if they
are > 25% identical.  It does a rigorous alignment.

	I would be very cautious about successive pairwise alignment schemes,
such as the Feng-Doolittle method (Pileup) and Clustal.  Any multiple
alignment method, including MSA, can do well on sequences with very
few gaps.  The reason you need a multiple alignment is to rationally
place gaps based on the information from several sequences. Pairwise
schemes can have serious problems in appropriately weighting large
gaps in multiple alignments.  I am familiar with one Feng-Doolittle
tree in the literature which is very unlikely to be correct, because
most of the topology was defined by gap weights.

Bill Pearson

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