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We present an algorithm--a generalization of the Needleman-Wunsch-Sellers algorithm--which finds within longer sequences all subsequences that resemble one another locally. The probability that so close a resemblance would occur by chance alone is calculated and used to classify these local homologies according to statistical significance. Repeats and… (More)

An interactive system for computer analysis of nucleic acid and protein sequences has been developed for the Los Alamos DNA Sequence Database. It provides a convenient way to search or verify various sequence features, e.g., restriction enzyme sites, protein coding frames, and properties of coded proteins. Further, the comprehensive analysis package on a… (More)

We present a method for calculating all possible single hairpin loop secondary structures in a nucleic acid sequence by the order of N2 operations where N is the total number of bases. Each structure may contain any number of bulges and internal loops. Most natural sequences are found to be indistinguishable from random sequences in the potential of forming… (More)

Multiple measures of similarity were employed to detect weak homologies among protein sequences (e.g., below 30% residue identity). A set of thresholds was empirically determined, by using sample proteins of known structure, so as to select only correct pairs of sequences; correct or incorrect alignment of sequences was judged by direct comparison of… (More)

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