Consistency of optimal sequence alignments.
Pairwise optimal alignments between three or more sequences are not necessarily consistent as a whole, but consistent and inconsistent residues are usually distributed in clusters. An efficient method has been developed for locating consistent regions when each pairwise alignment is given in the form of a "skeletal representation" (Bull. math. Biol. 52, 359-373). This method is further extended so that the combination of pairwise alignments that gives the greatest consistency is found when possibly many alignments are equally optimal for each pairwise comparison. A method for acceleration of simultaneous multiple sequence alignment is proposed in which consistent regions serve as "anchor points" limiting application of direct multi-way alignment to the rest of "inconsistent" regions.
Graduate School of Biomedical Sciences, University of Texas, Houston 77225.
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D000465:Algorithms; D001483:Base Sequence; D008969:Molecular Sequence Data; D012313:RNA; D012689:Sequence Homology, Nucleic Acid
D012313:RNA