Indexing Strategies for Rapid Searches of Short Words in Genome Sequences

@article{Iseli2007IndexingSF,
  title={Indexing Strategies for Rapid Searches of Short Words in Genome Sequences},
  author={Christian Iseli and Giovanna Ambrosini and Philipp Bucher and C. Victor Jongeneel},
  journal={PLoS ONE},
  year={2007},
  volume={2},
  pages={82 - 86}
}
Searching for matches between large collections of short (14-30 nucleotides) words and sequence databases comprising full genomes or transcriptomes is a common task in biological sequence analysis. We investigated the performance of simple indexing strategies for handling such tasks and developed two programs, fetchGWI and tagger, that index either the database or the query set. Either strategy outperforms megablast for searches with more than 10,000 probes. FetchGWI is shown to be a versatile… CONTINUE READING

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