Classification of DNA sequences using Bloom filters.
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.
Stranneheim
Henrik
H
Science for Life Laboratory, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden. henrik.stranneheim@biotech.kth.se
Käller
Max
M
Allander
Tobias
T
Andersson
Björn
B
Arvestad
Lars
L
Lundeberg
Joakim
J
D000465:Algorithms; D054629:Genome, Mitochondrial; D006801:Humans; D054892:Metagenome; D012137:Respiratory System / Q000382:microbiology; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA
Genome Res. 2001 Oct;11(10):1725-9
11591649
Bioinformatics. 2009 Jul 15;25(14):1754-60
19451168
Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12891-6
16118271
Genome Biol. 2009;10(3):R25
19261174
PLoS Biol. 2007 Mar;5(3):e77
17355176
PLoS Comput Biol. 2009 May;5(5):e1000386
19461883
Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11609-14
11562506
Bioinformatics. 2008 Mar 1;24(5):713-4
18227114
Nature. 2005 Sep 15;437(7057):376-80
16056220
Nat Biotechnol. 2008 Jul;26(7):779-85
18612301
PLoS One. 2008 Oct 08;3(10):e3373
18841204
Genome Res. 2008 Nov;18(11):1851-8
18714091
Genome Res. 2002 Apr;12(4):656-64
11932250
J Comput Biol. 2000 Feb-Apr;7(1-2):203-14
10890397
Nature. 2008 Nov 6;456(7218):66-72
18987736