AUTHOR=Gagie Travis , Puglisi Simon J. TITLE=Searching and Indexing Genomic Databases via Kernelization JOURNAL=Frontiers in Bioengineering and Biotechnology VOLUME=3 YEAR=2015 URL=https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2015.00012 DOI=10.3389/fbioe.2015.00012 ISSN=2296-4185 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.