Branch-and-cut approach to physical mapping with end-probes

Thomas Christof, Michael Juenger, John Kececioglu, Petra Mutzel, Gerhard Reinelt

Research output: Contribution to conferencePaper

16 Scopus citations

Abstract

A fundamental problem in computational biology is the construction of physical maps of chromosomes from hybridization experiments between unique probes and clones of chromosome fragments in the presence of error. Alizadeh, Karp, Weisser and Zweig [AKWZ94] first considered a maximum-likelihood model of the problem that is equivalent to finding an ordering of the probes that minimizes a weighted sum of errors, and developed several effective heuristics. We show that by exploiting information about the end-probes of clones, this model can be formulated as a weighted Betweenness Problem. This affords the significant advantage of allowing the well-developed tools of integer linear-programming and branch-and-cut algorithms to be brought to bear on physical mapping, enabling us for the first time to solve small mapping instances to optimality even in the presence of high error. We also show that by combining the optimal solution of many small overlapping Betweenness Problems, one can effectively screen errors from larger instances, and solve the edited instance to optimality as a Hamming-Distance Traveling Salesman Problem. This suggests a new combined approach to physical map construction.

Original languageEnglish (US)
Pages84-92
Number of pages9
StatePublished - Jan 1 1997
Externally publishedYes
EventProceedings of the 1997 1st Annual International Conference on Computational Molecular Biology, RECOMB - Santa Fe, NM, USA
Duration: Jan 20 1997Jan 23 1997

Other

OtherProceedings of the 1997 1st Annual International Conference on Computational Molecular Biology, RECOMB
CitySanta Fe, NM, USA
Period1/20/971/23/97

ASJC Scopus subject areas

  • Engineering(all)

Fingerprint Dive into the research topics of 'Branch-and-cut approach to physical mapping with end-probes'. Together they form a unique fingerprint.

  • Cite this

    Christof, T., Juenger, M., Kececioglu, J., Mutzel, P., & Reinelt, G. (1997). Branch-and-cut approach to physical mapping with end-probes. 84-92. Paper presented at Proceedings of the 1997 1st Annual International Conference on Computational Molecular Biology, RECOMB, Santa Fe, NM, USA, .