Construction of physical maps from oligonucleotide fingerprints data

Guy Mayraz, Ron Shamir

Research output: Contribution to journalArticlepeer-review

Abstract

A new algorithm for the construction of physical maps from hybridization fingerprints of short oligonucleotide probes has been developed. Extensive simulations in high-noise scenarios show that the algorithm produces an essentially completely correct map in over 95% of trials. Tests for the influence of specific experimental parameters demonstrate that the algorithm is robust to both false positive and false negative experimental errors. The algorithm was also tested in simulations using real DNA sequences of C. elegans, E. coli, S. cerevisiae, and H. sapiens. To overcome the non- randomness of probe frequencies in these sequences, probes were preselected based on sequence statistics and a screening process of the hybridization data was developed. With these modifications, the algorithm produced very encouraging results.

Original languageEnglish
Pages (from-to)237-252
Number of pages16
JournalJournal of Computational Biology
Volume6
Issue number2
DOIs
StatePublished - 1999

Keywords

  • Algorithms
  • Bayesian analysis
  • Finger printing
  • Hybridization
  • Oligonucleotides
  • Physical mapping

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