Parametric sequence comparisons. | Zendy

Michael S. Waterman | Zendy; Mark Eggert | Zendy; Eric S. Lander | Zendy

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Parametric sequence comparisons.

Author(s) -

Michael S. Waterman,

Mark Eggert,

Eric S. Lander

Publication year - 1992

Publication title -

proceedings of the national academy of sciences

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 5.011

H-Index - 771

eISSN - 1091-6490

pISSN - 0027-8424

DOI - 10.1073/pnas.89.13.6090

Subject(s) - computer science , sequence (biology) , dynamic programming , algorithm , multiple sequence alignment , parametric statistics , current (fluid) , mathematical optimization , sequence alignment , mathematics , biology , peptide sequence , statistics , genetics , gene , electrical engineering , engineering , biochemistry

Current algorithms can find optimal alignments of two nucleic acid or protein sequences, often by using dynamic programming. While the choice of algorithm penalty parameters greatly influences the quality of the resulting alignments, this choice has been done in an ad hoc manner. In this work, we present an algorithm to efficiently find the optimal alignments for all choices of the penalty parameters. It is then possible to systematically explore these alignments for those with the most biological or statistical interest. Several examples illustrate the method.

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