Construction of physical maps from oligonucleotide fingerprints data.
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.
Department of Computer Science, Sackler Faculty of Exact Sciences, Tel-Aviv University, Israel.
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Mayraz
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Shamir
D000465:Algorithms; D000818:Animals; D001499:Bayes Theorem; D017173:Caenorhabditis elegans / Q000235:genetics; D019295:Computational Biology; D003198:Computer Simulation; D020451:Contig Mapping / Q000379:methods; D016172:DNA Fingerprinting; D004926:Escherichia coli / Q000235:genetics; D016678:Genome; D006801:Humans; D015233:Models, Statistical; D008970:Molecular Weight; D009693:Nucleic Acid Hybridization; D015345:Oligonucleotide Probes / Q000235:genetics; D020161:Physical Chromosome Mapping / Q000379:methods*; D016012:Poisson Distribution; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012680:Sensitivity and Specificity
D015345:Oligonucleotide Probes