title: A fast and efficient algorithm for mapping short sequences to a reference genome.
abstract: Novel high-throughput (Deep) sequencing technology methods have redefined the way genome sequencing is performed. They are able to produce tens of millions of short sequences (reads) in a single experiment and with a much lower cost than previous sequencing methods. In this paper, we present a new algorithm for addressing the problem of efficiently mapping millions of short reads to a reference genome. In particular, we define and solve the Massive Approximate Pattern Matching problem for mapping short sequences to a reference genome.
authors.affiliation: Department of Computer Science, University of Cyprus, Nicosia, Cyprus. panton@cs.ucy.ac.cy
authors.forename: Pavlos
authors.initials: P
authors.lastname: Antoniou
authors.forename: Costas S
authors.initials: CS
authors.lastname: Iliopoulos
authors.forename: Laurent
authors.initials: L
authors.lastname: Mouchard
authors.forename: Solon P
authors.initials: SP
authors.lastname: Pissis
mesh_terms: D000465:Algorithms; D000818:Animals; D002874:Chromosome Mapping / Q000706:statistics & numerical data*; D019295:Computational Biology; D023281:Genomics / Q000706:statistics & numerical data*; D051379:Mice; D010363:Pattern Recognition, Automated / Q000706:statistics & numerical data; D012313:RNA / Q000235:genetics; D016415:Sequence Alignment / Q000706:statistics & numerical data*; D014960:X Chromosome / Q000235:genetics
chemical_list: D012313:RNA