A branch and bound algorithm for local multiple alignment.

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Abstract

A Branch and Bound Algorithm has been developed to find a set of window positions in a compilation of sequences with globally maximal information content. We have also developed an algorithm for brute force evaluation of solutions which is faster by a factor of the length of the windows than the naïve brute force algorithm. The combination of these two algorithms allows us to solve problems to optimality that were previously amenable only to heuristic algorithms.

Original languageEnglish
Pages (from-to)368-383
Number of pages16
JournalPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Publication statusPublished - 1996 Jan 1

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All Science Journal Classification (ASJC) codes

  • Biomedical Engineering
  • Computational Theory and Mathematics

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