Journal of Molecular Biology
Volume 243, Issue 4, 4 November 1994, Pages 574-578
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Communication
Position-based sequence weights

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Abstract

Sequence weighting methods have been used to reduce redundancy and emphasize diversity in multiple sequence alignment and searching application. 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 distane measure. These position-based weights make minimal assumptions, are simple to compute, and perform well comprehensive evaluations.

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This work was supported by a grant from the National Institutes of Health (GM29009).

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We thank Bill Alford for programming help and Toby Gibson for comments on the manuscript.

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