AN ADAPTIVE, OBJECT-ORIENTED STRATEGY FOR BASE CALLING IN DNA-SEQUENCE ANALYSIS

An algorithm has been developed for the determination of nucleotide se quence from data produced in fluorescence-based automated DNA sequenci ng instruments employing the four-color strategy. This algorithm takes advantage of object oriented programming techniques for modularity an d extensibility. The algorithm is adaptive in that data sets from a wi de variety of instruments and sequencing conditions can be used with g ood results. Confidence values are provided on the base calls as an es timate of accuracy. The algorithm iteratively employs confidence deter minations from several different modules, each of which examines a dif ferent feature of the data for accurate peak identification. Modules w ithin this system can be added or removed for increased performance or for application to a different task. In comparisons with commercial s oftware, the algorithm performed well.