slaMEM: efficient retrieval of maximal exact matches using a sampled LCP array

@article{Fernandes2014slaMEMER,
  title={slaMEM: efficient retrieval of maximal exact matches using a sampled LCP array},
  author={Francisco Fernandes and Ana T. Freitas},
  journal={Bioinformatics},
  year={2014},
  volume={30 4},
  pages={464-71}
}
MOTIVATION Maximal exact matches, or just MEMs, are a powerful tool in the context of multiple sequence alignment and approximate string matching. The most efficient algorithms to collect them are based on compressed indexes that rely on longest common prefix array-centered data structures. However, their space-efficient representations make use of encoding techniques that are expensive from a computational point of view. With the deluge of data generated by high-throughput sequencing, new… CONTINUE READING
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