Mapping cDNA sequences to genomic sequences

摘要

A rapid mapping of cDNA sequences on genomic sequences. The genome sequence is divided into a sequence of k-base characters which are not overlapped with each other, and the coordinates on the genome array where each k-mer appears are stored in the table. This table is used to pair all k-mers on the cDNA and the k-mer on the genome array. A set of k-mer pairs, which correspond to the correct mapping rather than coincidence, is identified at high speed using an efficient solution of the problem of extracting the longest monotonic increment in the sequence. The k-mer pair corresponding to the mapping thus obtained is extended to the corresponding base by array alignment, and then corrected in the splice site. Furthermore, to provide an optimal parameter selection, an interactive interface capable of real-time response is provided. Diagram