A metric model of amino acid substitution | Zendy

Weijia Xu | Zendy; Daniel P. Miranker | Zendy

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A metric model of amino acid substitution

Author(s) -

Weijia Xu,

Daniel P. Miranker

Publication year - 2004

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bth065

Subject(s) - metric (unit) , computer science , homology (biology) , substitution (logic) , sequence (biology) , sequence alignment , algorithm , mathematics , peptide sequence , genetics , amino acid , biology , operations management , gene , economics , programming language

We address the question of whether there exists an effective evolutionary model of amino-acid substitution that forms a metric-distance function. There is always a trade-off between speed and sensitivity among competing computational methods of determining sequence homology. A metric model of evolution is a prerequisite for the development of an entire class of fast sequence analysis algorithms that are both scalable, O(log n) and sensitive.

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