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Reports (Research Report) Year : 2009

Flexible Alignments for Protein Threading


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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Dates and versions

inria-00355546 , version 1 (23-01-2009)


  • HAL Id : inria-00355546 , version 1
  • PRODINRA : 250027


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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