title: Classification of DNA sequences using Bloom filters.
abstract: BACKGROUND
  New generation sequencing technologies producing increasingly complex datasets demand new efficient and specialized sequence analysis algorithms. Often, it is only the 'novel' sequences in a complex dataset that are of interest and the superfluous sequences need to be removed.
  
  
  RESULTS
  A novel algorithm, fast and accurate classification of sequences (FACSs), is introduced that can accurately and rapidly classify sequences as belonging or not belonging to a reference sequence. FACS was first optimized and validated using a synthetic metagenome dataset. An experimental metagenome dataset was then used to show that FACS achieves comparable accuracy as BLAT and SSAHA2 but is at least 21 times faster in classifying sequences.
  
  
  BACKGROUND
  Source code for FACS, Bloom filters and MetaSim dataset used is available at http://facs.biotech.kth.se. The Bloom::Faster 1.6 Perl module can be downloaded from CPAN at http://search.cpan.org/ approximately palvaro/Bloom-Faster-1.6/
  
  
  BACKGROUND
  henrik.stranneheim@biotech.kth.se; joakiml@biotech.kth.se
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Science for Life Laboratory, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden. henrik.stranneheim@biotech.kth.se
authors.forename: Henrik
authors.initials: H
authors.lastname: Stranneheim
authors.forename: Max
authors.initials: M
authors.lastname: Käller
authors.forename: Tobias
authors.initials: T
authors.lastname: Allander
authors.forename: Björn
authors.initials: B
authors.lastname: Andersson
authors.forename: Lars
authors.initials: L
authors.lastname: Arvestad
authors.forename: Joakim
authors.initials: J
authors.lastname: Lundeberg
mesh_terms: D000465:Algorithms; D054629:Genome, Mitochondrial; D006801:Humans; D054892:Metagenome; D012137:Respiratory System / Q000382:microbiology; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA
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