Likelihood DNA sequencing by hybridization

Sequencing by hybridization (SBH) extracts local sequence information from a DNA fragment using hybridization with oligonucleotides and then reconstructs the sequence using the derived information. We describe an improvement to the SBH methodology which will allow it to work efficiently in the presence of hybridization errors. In particular, given a set of hybridizing probes, and the empirically derived rates of false positive and false negative hybridization, we can estimate the most likely DNA fragment to have produced the set of probes, and then estimate the probability that it generated the hybridization data. This methodology extends earlier results by identifying the most probable fragment to have generated the actual hybridization data. The methodology described will also generate longer unambiguous sequence fragments without the use of overlapping fragments.