Genome-wide synteny through highly sensitive sequence alignment: Satsuma.

Abstract

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.

Citation

Manfred Grabherr, Pamela Russell, Miriah Meyer, Evan Mauceli, Jessica Alfoldi, Federica Di Palma, Kerstin Lindblad-Toh
Genome-wide synteny through highly sensitive sequence alignment: Satsuma.
Bioinformatics, 26(9):1145-1151, doi:10.1093/bioinformatics/btq102, 2010.

Satsuma screenshot

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