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Flexible Alignments for Protein Threading
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.
Cited literature [8 references]
https://hal.inria.fr/inria-00355546
Contributor : Guillaume Collet Connect in order to contact the contributor
Submitted on : Friday, January 23, 2009 - 10:18:37 AM
Last modification on : Wednesday, September 8, 2021 - 3:30:37 AM
Long-term archiving on: : Tuesday, June 8, 2010 - 9:13:02 PM
Contributor : Guillaume Collet Connect in order to contact the contributor
Submitted on : Friday, January 23, 2009 - 10:18:37 AM
Last modification on : Wednesday, September 8, 2021 - 3:30:37 AM
Long-term archiving on: : Tuesday, June 8, 2010 - 9:13:02 PM
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RR-6808.pdf
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