Journal
BIOINFORMATICS
Volume 26, Issue 9, Pages 1145-1151Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btq102
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Funding
- National Human Genome Research Institute [NIH 1 U54 HG03067]
- ESF
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Motivation: Comparative genomics heavily relies on alignments of large and often complex DNA sequences. From an engineering perspective, the problem here is to provide maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to accommodate the billions of base pairs of vertebrate genomes). Results: Satsuma addresses all three issues through novel strategies: (i) cross-correlation, implemented via fast Fourier transform; (ii) a match scoring scheme that eliminates almost all false hits; and (iii) an asynchronous 'battleship'-like search that allows for aligning two entire fish genomes (470 and 217 Mb) in 120 CPU hours using 15 processors on a single machine.
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