期刊
BIOINFORMATICS
卷 34, 期 24, 页码 4290-4292出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/bty506
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资金
- Faculty of Electrical, Electronic, Computer and Control Engineering, Lodz University of Technology [501/12-24-1-5418]
- OP VVV project Research Center for Informatics [CZ.02.1.01/0.0/0.0/16_019/0000765]
Motivation: The many thousands of high-quality genomes available now-a-days imply a shift from single genome to pan-genomic analyses. A basic algorithmic building brick for such a scenario is online search over a collection of similar texts, a problem with surprisingly few solutions presented so far. Results: We present SOPanG, a simple tool for exact pattern matching over an elastic-degenerate string, a recently proposed simplified model for the pan-genome. Thanks to bit-parallelism, it achieves pattern matching speeds above 400 MB/s, more than an order of magnitude higher than of other software.
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