SOPanG: online text searching over a pan-genome.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 29939210.
- Also identified by DOI 10.1093/bioinformatics/bty506.
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Abstract
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. 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. SOPanG is available for free from: https://github.com/MrAlexSee/sopang. Supplementary data are available at Bioinformatics online.
Medical subject headings
- Genome
- Genomics
- Software