Discriminative modelling of context-specific amino acid substitution probabilities | Zendy

Christof Angermüller | Zendy; A. Biegert | Zendy; Johannes Söding | Zendy

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Discriminative modelling of context-specific amino acid substitution probabilities

Author(s) -

Christof Angermüller,

A. Biegert,

Johannes Söding

Publication year - 2012

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/bts622

Subject(s) - discriminative model , substitution (logic) , computer science , context (archaeology) , sequence alignment , benchmark (surveying) , sequence (biology) , probabilistic logic , artificial intelligence , multiple sequence alignment , computational biology , pattern recognition (psychology) , machine learning , peptide sequence , biology , genetics , programming language , paleontology , gene , geodesy , geography

Protein sequence searching and alignment are fundamental tools of modern biology. Alignments are assessed using their similarity scores, essentially the sum of substitution matrix scores over all pairs of aligned amino acids. We previously proposed a generative probabilistic method that yields scores that take the sequence context around each aligned residue into account. This method showed drastically improved sensitivity and alignment quality compared with standard substitution matrix-based alignment.

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