METHOD AND SYSTEM FOR EVALUATING SEQUENCES

摘要

A method of evaluating correlation between sequences by employing a hierarchy of evaluation algorithms. The evaluation algorithms may be arranged in order of computational efficiency as specified by a user or as determined by the system. The algorithms may range from a simple equality algorithm through to seeded alignment algorithms etc.;Distributed and parallel processing systems may be employed in the method of the invention in graphical processing units may be employed.;The method may be employed with a wide range of sequencers including sequencers produced by Illumina Inc Complete Genomics Inc. and Pacific Biosciences Inc.

主权项

1. A computer implemented method of evaluating the correlation between a plurality of sample sequences and a reference sequence using a plurality of evaluation algorithms, comprising applying the evaluation algorithms in an order designed to minimise the processing time for evaluating the correlation, wherein the plurality of evaluation algorithms comprises:
a lower-bound algorithm which rejects alignments of the sample sequences in unmodified form to the reference sequence if an alignment quality threshold is not satisfied; and a modified sequence alignment algorithm in which the sample sequences are modified at potential alignment positions with the reference sequence, with the set of modifications of the sample sequence comprising an insertion.