PT  - JOURNAL ARTICLE
AU  - Travis Gagie
AU  - Simon J. Puglisi
TI  - Searching and Indexing Genomic Databases via Kernelization
AID  - 10.1101/012161
DP  - 2014 Jan 01
TA  - bioRxiv
PG  - 012161
4099  - http://biorxiv.org/content/early/2014/12/04/012161.short
4100  - http://biorxiv.org/content/early/2014/12/04/012161.full
AB  - 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.