Construction of physical maps from oligonucleotide fingerprints data

A new algorithm for the construction of physical maps from hybridization fi ngerprints of short oligonucleotide probes has been developed. Extensive si mulations in high-noise scenarios show that the algorithm produces an essen tially completely correct map in over 95% of trials. Tests for the influenc e of specific experimental parameters demonstrate that the algorithm is rob ust to both false positive and false negative experimental errors. The algo rithm 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 seq uence statistics and a screening process of the hybridization data was deve loped. With these modifications, the algorithm produced very encouraging re sults.