A novel algorithm, FACS (Fast and Accurate Classification of Sequences), is introduced that can accurately and rapidly align sequences 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 is at least three times faster and more accurate than BLAT and SSAHA2 in classifying sequences when using references larger than 50Mbp.
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Stranneheim H, Käller M, Allander T, Andersson B, Arvestad L, Lundeberg J.
Classification of DNA sequences using Bloom filters.
Bioinformatics, 2010 July 1; 26(13):1595-1600. Published online 2010 May 13. doi:10.1093/bioinformatics/btq230