A branch-and-cut algorithm for multiple sequence alignment - download pdf or read online

By Althaus E.

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In almost all cases, either the optimal LP solution was integer, or the time limit was exceeded during the solution of the LP at the root node. Note that the time limit was not checked during calls to the LP solver, so the overall running time could exceed the 10 hours time limit. 6 out of 7 minutes for instance 1hpi. For all the instances, separation took less than 10 seconds for each iteration, whereas the time to solve the LPs heavily depended on the number of variables that remained in the LP after preprocessing.

Biol. 302, 205–217 (2000) 23. : A Polyhedral Approach to Sequence Alignment Problems. PhD thesis, Universit¨at des Saarlandes, 1999 24. : A branch-and-cut algorithm for multiple sequence alignment. In: Proceedings of the First Annual International Conference on Computational Molecular Biology (RECOMB-97), 1997, pp 241–249 25. K. Reinert, J. Stoye, and T. Will. An iterative methods for faster sum-of-pairs multiple sequence alignment. BIOINFORMATICS 16(9):808–814, 2000. 26. SCIL–Symbolic Constraints for Integer Linear programming, 2002.

This work was partially supported by a fellowship within the ICSI Postdoc Program of the German Academic Exchange Service (DAAD), and by the German Federal Ministry of Education and Research, grant no. 0312705A “Berlin Center for Genome Based Bioinformatics”. Moreover, part of this work was done while the second author was visiting the Max Planck Institut f¨ur Informatik in Saarbr¨ucken. References 1. : SCIP - a framework to integrate constraint and mixed integer programming. Technical Report 04-19, Zuse Institute Berlin, 2004.

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A branch-and-cut algorithm for multiple sequence alignment by Althaus E.

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