RAPSearch 2 : a fast and memory-efficient protein similarity search tool for next-generation sequencing data

@inproceedings{Zhao2011RAPSearch2,
  title={RAPSearch 2 : a fast and memory-efficient protein similarity search tool for next-generation sequencing data},
  author={Yongan Zhao and Haixu Tang and Yuzhen Ye},
  year={2011}
}
Summary: With the wide application of next-generation sequencing (NGS) techniques, fast tools for protein similarity search that scale well to large query datasets and large databases are highly desirable. In a previous work, we developed RAPSearch, an algorithm that achieved a ∼20–90-fold speedup relative to BLAST while still achieving similar levels of sensitivity for short protein fragments derived from NGS data. RAPSearch, however, requires a substantial memory footprint to identify… CONTINUE READING
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