Answering biological questions by querying k-mer databases

@article{Greenfield2013AnsweringBQ,
  title={Answering biological questions by querying k-mer databases},
  author={Paul Greenfield and Uwe R{\"o}hm},
  journal={Concurrency and Computation: Practice and Experience},
  year={2013},
  volume={25},
  pages={497-509}
}
This paper describes a k-mer approach to analysing DNA data and quickly answering certain types of ad hoc biological questions. These k-mers (short DNA strings) are stored in a conventional relational database and indexed to support efficient exact match operations. We show that k-mers around 20–25 bases long have interesting and useful uniqueness properties that can be used to compute a ‘relatedness’ metric and also allow k-mers to be used as ‘unique enough’ tags to identify organisms and… CONTINUE READING
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