title: Searching and Indexing Genomic Databases via Kernelization.
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 20-year history of this idea and discuss its relation to kernelization in parameterized complexity.
authors.affiliation: Helsinki Institute for Information Technology (HIIT) and Department of Computer Science, University of Helsinki , Helsinki , Finland.
authors.forename: Travis
authors.initials: T
authors.lastname: Gagie
authors.affiliation: Helsinki Institute for Information Technology (HIIT) and Department of Computer Science, University of Helsinki , Helsinki , Finland.
authors.forename: Simon J
authors.initials: SJ
authors.lastname: Puglisi
keywords: approximate pattern matching; data compression; genomic databases; indexing; kernelization; random-access reading; string algorithms