Improvements on bicriteria pairwise sequence alignment: algorithms and applications | Zendy

Maryam Abbasi | Zendy; Luís Paquete | Zendy; Arnaud Liefooghe | Zendy; Miguel Pinheiro | Zendy; Pedro M. C. Matias | Zendy

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Improvements on bicriteria pairwise sequence alignment: algorithms and applications

Author(s) -

Maryam Abbasi,

Luís Paquete,

Arnaud Liefooghe,

Miguel Pinheiro,

Pedro M. C. Matias

Publication year - 2013

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/btt098

Subject(s) - pairwise comparison , computer science , pruning , sequence (biology) , multiple sequence alignment , algorithm , dynamic programming , code (set theory) , source code , phylogenetic tree , sequence alignment , artificial intelligence , programming language , set (abstract data type) , gene , agronomy , peptide sequence , biology , biochemistry , genetics , chemistry

In this article, we consider the bicriteria pairwise sequence alignment problem and propose extensions of dynamic programming algorithms for several problem variants with a novel pruning technique that efficiently reduces the number of states to be processed. Moreover, we present a method for the construction of phylogenetic trees based on this bicriteria framework. Two exemplary cases are discussed.

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