essaMEM: finding maximal exact matches using enhanced sparse suffix arrays.
other · Level V
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- Record sourced from PubMed, PMID 23349213.
- Also identified by DOI 10.1093/bioinformatics/btt042.
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Abstract
We have developed essaMEM, a tool for finding maximal exact matches that can be used in genome comparison and read mapping. essaMEM enhances an existing sparse suffix array implementation with a sparse child array. Tests indicate that the enhanced algorithm for finding maximal exact matches is much faster, while maintaining the same memory footprint. In this way, sparse suffix arrays remain competitive with the more complex compressed suffix arrays.
Medical subject headings
- Sequence Analysis
- Software