Flexible Alignments for Protein Threading

Guillaume Collet 1 Rumen Andonov 1 Nicola Yanev 1 Jean-François Gibrat 2
1 SYMBIOSE - Biological systems and models, bioinformatics and sequences
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, Inria Rennes – Bretagne Atlantique
Abstract : We present a new local alignment method for the protein threading problem. Local sequence-sequence alignments are widely used to find functionally important regions in families of proteins. However, to the best of our knowledge, no local sequence-structure alignment algorithm has been described in the literature. Here we model local alignments as Mixed Integer Programming (MIP) models. These models permit to align a part of a protein structure onto a protein sequence in order to detect local similarities. The paper describes two MIP models, compares and analyzes their performance by using ILOG CPLEX 10 solver.
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Guillaume Collet, Rumen Andonov, Nicola Yanev, Jean-François Gibrat. Flexible Alignments for Protein Threading. [Research Report] RR-6808, INRIA. 2009. ⟨inria-00355546⟩

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