@article {18989,
	title = {Reducing storage requirements for biological sequence comparison},
	journal = {BioinformaticsBioinformatics},
	volume = {20},
	year = {2004},
	month = {2004/12/12/},
	pages = {3363 - 3369},
	abstract = {Motivation: Comparison of nucleic acid and protein sequences is a fundamental tool of modern bioinformatics. A dominant method of such string matching is the {\textquoteleft}seed-and-extend{\textquoteright} approach, in which occurrences of short subsequences called {\textquoteleft}seeds{\textquoteright} are used to search for potentially longer matches in a large database of sequences. Each such potential match is then checked to see if it extends beyond the seed. To be effective, the seed-and-extend approach needs to catalogue seeds from virtually every substring in the database of search strings. Projects such as mammalian genome assemblies and large-scale protein matching, however, have such large sequence databases that the resulting list of seeds cannot be stored in RAM on a single computer. This significantly slows the matching process.Results: We present a simple and elegant method in which only a small fraction of seeds, called {\textquoteleft}minimizers{\textquoteright}, needs to be stored. Using minimizers can speed up string-matching computations by a large factor while missing only a small fraction of the matches found using all seeds.
},
	isbn = {1367-4803, 1460-2059},
	doi = {10.1093/bioinformatics/bth408},
	url = {http://bioinformatics.oxfordjournals.org/content/20/18/3363},
	author = {Roberts,Michael and Hayes,Wayne and Hunt,Brian R. and Mount, Stephen M. and Yorke,James A.}
}
