Solving multiple sequence alignment problem utilizing integer linear programming
(Universitas Indonesia, 2008)
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| One of the dominant problems in computational molecular biology ismultiple sequence alignment (MSA) of DNA. Many methods have beenproposed to solve MSA problem such as dynamic programming and heuristic.A method has been proposed by Althaus et al. to solve MSA problem which isbased on integer linear programming (ILP). The general ILP formulation ofthe MSA is derived from the graph representation of the MSA problem.Although we have the general ILP formulation of the MSA problem,constructing the ILP model of an MSA that can be solved directly using anILP solver is not straightforward. We develop a MATLAB program that cangenerate and solve the ILP model of an MSA problem. The method that isused to solve the ILP model is branch-and-bound. The constructed programcan generate the ILP model of any given MSA problem but can only solve anMSA problem of a small number of short DNA sequences. The result of theprogram is the aligned sequences of the MSA problem. |
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| No. Panggil : | S-Pdf |
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| Penerbitan : | [Place of publication not identified]: Universitas Indonesia, 2008 |
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| Bahasa : | Eng. |
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| Deskripsi Fisik : | xiv, 89 hlm. ; 30 cm. + Lamp. |
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| Lembaga Pemilik : | Universitas Indonesia |
| Lokasi : | Perpustakaan UI, Lantai 3 |
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| S-Pdf | TERSEDIA |
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