Suboptimal sequence alignment in molecular biology. Alignment with error analysis.
A molecular sequence alignment algorithm based on dynamic programming has been extended to allow the computation of all pairs of residues that can be part of optimal and suboptimal sequence alignments. The uncertainties inherent in sequence alignment can be displayed using a new form of dot plot. The method allows the qualitative assessment of whether or not two sequences are related, and can reveal what parts of the alignment are better determined than others. It also permits the computation of representative optimal and suboptimal alignments. The relation between alignment reliability and alignment parameters is discussed. Other applications are to cyclical permutations of sequences and the detection of self-similarity. An application to multiple sequence alignment is noted.
Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ontario.
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Zuker
D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D006801:Humans; D008967:Molecular Biology / Q000379:methods; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid
D011506:Proteins