Network-based filtering of unreliable markers in genome mapping

Omar Al-Azzam, Loai Alnemer, Charith Chitraranjan, Anne M. Denton, Ajay Kumar, Filippo Bassi, Muhammad J. Iqbal, Shahryar F. Kianian

Research output: Chapter in Book/Report/Conference proceedingConference contribution

5 Scopus citations

Abstract

Genome mapping, or the experimental determination of the ordering of DNA markers on a chromosome, is an important step in genome sequencing and ultimate assembly of sequenced genomes. The presented research addresses the problem of identifying markers that cannot be placed reliably. If such markers are included in standard mapping procedures they can result in an overall poor mapping. Traditional techniques for identifying markers that cannot be placed consistently are based on resampling, which requires an already computationally expensive process to be done for a large ensemble of resampled populations. We propose a network-based approach that uses pair wise similarities between markers and demonstrate that the results from this approach largely match the more computationally expensive conventional approaches. The evaluation of the proposed approach is done on data from the radiation hybrid mapping of the wheat genome.

Original languageEnglish (US)
Title of host publicationProceedings - 10th International Conference on Machine Learning and Applications, ICMLA 2011
Pages19-24
Number of pages6
DOIs
StatePublished - 2011
Event10th International Conference on Machine Learning and Applications, ICMLA 2011 - Honolulu, HI, United States
Duration: Dec 18 2011Dec 21 2011

Publication series

NameProceedings - 10th International Conference on Machine Learning and Applications, ICMLA 2011
Volume1

Other

Other10th International Conference on Machine Learning and Applications, ICMLA 2011
CountryUnited States
CityHonolulu, HI
Period12/18/1112/21/11

Keywords

  • LOD score
  • neighborhood matrix
  • similarity network
  • unreliable marker

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