Journal Article

Genome-wide synteny through highly sensitive sequence alignment: <i>Satsuma</i>

Manfred G. Grabherr, Pamela Russell, Miriah Meyer, Evan Mauceli, Jessica Alföldi, Federica Di Palma and Kerstin Lindblad-Toh

in Bioinformatics

Volume 26, issue 9, pages 1145-1151
Published in print May 2010 | ISSN: 1367-4803
Published online March 2010 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btq102
Genome-wide synteny through highly sensitive sequence alignment: Satsuma

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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.

Availability: 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/

Contact: grabherr@broadinstitute.org

Journal Article.  5632 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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