Dec 4, 2014

Searching and Indexing Genomic Databases via Kernelization

BioRxiv : the Preprint Server for Biology
Travis Gagie, Simon J Puglisi

Abstract

The rapid advance of DNA sequencing technologies has yielded databases of thousands of genomes. To search and index these databases effectively, it is important that we take advantage of the similarity between those genomes. Several authors have recently suggested searching or indexing only one reference genome and the parts of the other genomes where they differ. In this paper we survey the twenty-year history of this idea and discuss its relation to kernelization in parameterized complexity.

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Mentioned in this Paper

Genome
Genomics
Sequence Determinations, DNA
DNA Sequence
Expression Technologies for DNA and RNA

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