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Computing the Minimal Tiling Path from a Physical Map by Integer Linear Programming

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Algorithms in Bioinformatics (WABI 2008)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5251))

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Abstract

We study the problem of selecting the minimal tiling path (MTP) from a set of clones arranged in a physical map. We formulate the constraints of the MTP problem in a graph theoretical framework, and we derive an optimization problem that is solved via integer linear programming. Experimental results show that when we compare our algorithm to the commonly used software FPC, the MTP produced by our method covers a higher portion of the genome, even using a smaller number of MTP clones. These results suggest that if one would employ the MTP produced by our method instead of FPC’s in a clone-by-clone sequencing project, one would reduce by about 12% the sequencing cost.

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Author information

Authors and Affiliations

  1. Dept. of Computer Science and Eng., University of California, Riverside, CA,  

    Serdar Bozdag & Stefano Lonardi

  2. Dept. of Botany and Plant Sciences, University of California, Riverside, CA,  

    Timothy J Close

Authors
  1. Serdar Bozdag
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  2. Timothy J Close
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  3. Stefano Lonardi
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Editor information

Keith A. Crandall Jens Lagergren

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© 2008 Springer-Verlag Berlin Heidelberg

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Bozdag, S., Close, T.J., Lonardi, S. (2008). Computing the Minimal Tiling Path from a Physical Map by Integer Linear Programming. In: Crandall, K.A., Lagergren, J. (eds) Algorithms in Bioinformatics. WABI 2008. Lecture Notes in Computer Science(), vol 5251. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-87361-7_13

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  • DOI: https://doi.org/10.1007/978-3-540-87361-7_13

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-87360-0

  • Online ISBN: 978-3-540-87361-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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