Position-based sequence weights.
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.
Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98104.
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D000595:Amino Acid Sequence; D001483:Base Sequence; D003198:Computer Simulation; D016208:Databases, Factual; D014644:Genetic Variation; D008969:Molecular Sequence Data; D016415:Sequence Alignment