[Extraction of symbolic determinants common to a family of biological sequences].
A set of sequences can be defined by their common subsequences, and the length of these is a measure of the overall resemblance of the set. Each subsequence corresponds to a succession of symbols embedded in every sequence, following the same order but not necessarily contiguous. Determining the longest common subsequence (LCS) requires the exhaustive testing of all possible common subsequences, which sum up to about 2L, if L is the length of the shortest sequence. We present a polynomial algorithm (O(n X L4), where n is the number of sequences) for generating strings related to the LCS and constructed with the sequence alphabet and an indetermination symbol. Such strings are iteratively improved by deleting indetermination symbols and concomitantly introducing the greatest number of alphabet symbols. Processed accordingly, nucleic acid and protein sequences lead to key-words encompassing the salient positions of homologous chains, which can be used for aligning or classifying them, as well as for finding related sequences in data banks.
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W
Saurin
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P
Marlière
D000595:Amino Acid Sequence; D001483:Base Sequence; D003201:Computers; D004926:Escherichia coli / Q000235:genetics; D012329:RNA, Bacterial; D012343:RNA, Transfer; D012984:Software
D012329:RNA, Bacterial; D012343:RNA, Transfer
Extraction de déterminants symboliques communs à une famille de bioséquences.