Probe location in the presence of errors: a problem from DNA mapping Original Research Article

We consider the problem of mapping probes to locations along the genome given noisy pairwise distance data as input. The model used is quite general: The input consists of a collection of probe pairs and a distance interval for the genomic distance separating each pair. We call this the probe-location problem. Because the distance intervals are only known with some confidence level, some may be erroneous and must be identified and removed in order to find a consistent map. This is cast as the gang-filtering problem. To the authorʹs knowledge, this is a previously unstudied combinatorial problem that can be viewed as a generalization of classical group testing. A randomized algorithm for this problem is proposed. All the algorithms were implemented and experimental results were collected for synthetic data sets (with and without errors) and real data from a region of human chromosome 4.