Method that aligns cDNA sequences to genome sequences

摘要

Method and apparatus for mapping cDNA sequences to genome sequences at high speed are disclosed. A genome sequence is divided into K-base-length partial sequences that do not overlap and are continuous (K-mers). Then, they are stored in a table with coordinates on the genome sequence where each of them appears. Using this table, correspondences of K-mers are created from perfectly matching pairs of K-mers on the cDNA and the K-mers on the genome sequence. Of all the correspondences of K-mers, those sets that represent correct mapping rather than accidental coincidence are identified at high speed by a method based on a publicly known method that extracts a longest increasing partial sequence from a numerical sequence. The resultant correspondences of K-mers are extended to the association between bases by sequence alignment, and then correction at splice sites is performed. In order to allow for an optimum selection of parameters, an interactive interface capable of real-time response is provided.