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SeqWare Query Engine: storing and searching sequence data in the cloud PDF available through Get Fulltext Research

O’Connor, Brian D Merriman, Barry Nelson, Stanley F

Published in BMC Bioinformatics

BackgroundSince the introduction of next-generation DNA sequencers the rapid increase in sequencer throughput, and associated drop in costs, has resulted in more than a dozen human genomes being resequenced over the last few years. These efforts are merely a prelude for a future in which genome resequencing will be commonplace for both biomedical r...

Local alignment of two-base encoded DNA sequence PDF available through Get Fulltext Research

Homer, Nils Merriman, Barry Nelson, Stanley F

Published in BMC Bioinformatics

BackgroundDNA sequence comparison is based on optimal local alignment of two sequences using a similarity score. However, some new DNA sequencing technologies do not directly measure the base sequence, but rather an encoded form, such as the two-base encoding considered here. In order to compare such data to a reference sequence, the data must be d...

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