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


BACKGROUND
Satsuma is part of the Spines software package, implemented in C++ on Linux. The latest version of Spines can be freely downloaded under the LGPL license from http://www.broadinstitute.org/science/programs/genome-biology/spines/.
Grabherr
Manfred G
MG
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. grabherr@broadinstitute.org
Russell
Pamela
P
Meyer
Miriah
M
Mauceli
Evan
E
Alföldi
Jessica
J
Di Palma
Federica
F
Lindblad-Toh
Kerstin
K
D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D005583:Fourier Analysis; D016678:Genome; D023281:Genomics / Q000379:methods; D006801:Humans; D015233:Models, Statistical; D012275:Oryza / Q000235:genetics; D011336:Probability; D011381:Programming Languages; D016415:Sequence Alignment; D012984:Software; D045868:Sorghum / Q000235:genetics; D023721:Tetraodontiformes