Spliced Alignment

Given a genomic sequence and a set of candidate exons, the spliced alignment algorithm [3] explores all possible exon assemblies and finds a chain of exons which best fits a related target protein. The set of candidate exons is constructed by considering all blocks between candidate acceptor and donor sites (i.e., between AG dinucleotide at the intron-exon boundary and GU dinucleotide at exon-intron boundary) and further filtration of this set. To avoid losing true exons, the filtration procedure is designed to be very gentle, and the resulting set of blocks may contain a large number of false exons. Instead of trying to identify the correct exons by further pursuit of statistical methods, The algorithm considers all possible chains of candidate exons and finds a chain with the maximum global similarity to the target protein.