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J Mol Biol. 1994 Nov 4;243(4):574-8.

Position-based sequence weights.

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Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98104.


Sequence weighting methods have been used to reduce redundancy and emphasize diversity in multiple sequence alignment and searching applications. Each of these methods is based on a notion of distance between a sequence and an ancestral or generalized sequence. We describe a different approach, which bases weights on the diversity observed at each position in the alignment, rather than on a sequence distance measure. These position-based weights make minimal assumptions, are simple to compute, and perform well in comprehensive evaluations.

[Indexed for MEDLINE]

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