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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).<\/jats:p>\n               <jats:p>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 \u2018battleship\u2019-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.<\/jats:p>\n               <jats:p>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\/<\/jats:p>\n               <jats:p>Contact: \u00a0grabherr@broadinstitute.org<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq102","type":"journal-article","created":{"date-parts":[[2010,3,7]],"date-time":"2010-03-07T01:23:08Z","timestamp":1267924988000},"page":"1145-1151","source":"Crossref","is-referenced-by-count":325,"title":["Genome-wide synteny through highly sensitive sequence alignment: <i>Satsuma<\/i>"],"prefix":"10.1093","volume":"26","author":[{"given":"Manfred G.","family":"Grabherr","sequence":"first","affiliation":[{"name":"1 Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, 2 School of Engineering and Applied Sciences, Harvard University, 33 Oxford Street, Cambridge, MA 02138, USA and 3 Department of Medical Biochemistry and Microbiology, Uppsala University, Box 597, SE-751 24 Uppsala, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pamela","family":"Russell","sequence":"additional","affiliation":[{"name":"1 Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, 2 School of Engineering and Applied Sciences, Harvard University, 33 Oxford Street, Cambridge, MA 02138, USA and 3 Department of Medical Biochemistry and Microbiology, Uppsala University, Box 597, SE-751 24 Uppsala, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miriah","family":"Meyer","sequence":"additional","affiliation":[{"name":"1 Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, 2 School of Engineering and Applied Sciences, Harvard University, 33 Oxford Street, Cambridge, MA 02138, USA and 3 Department of Medical Biochemistry and Microbiology, Uppsala University, Box 597, SE-751 24 Uppsala, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evan","family":"Mauceli","sequence":"additional","affiliation":[{"name":"1 Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, 2 School of Engineering and Applied Sciences, Harvard University, 33 Oxford Street, Cambridge, MA 02138, USA and 3 Department of Medical Biochemistry and Microbiology, Uppsala University, Box 597, SE-751 24 Uppsala, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica","family":"Alf\u00f6ldi","sequence":"additional","affiliation":[{"name":"1 Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, 2 School of Engineering and Applied Sciences, Harvard University, 33 Oxford Street, Cambridge, MA 02138, USA and 3 Department of Medical Biochemistry and Microbiology, Uppsala University, Box 597, SE-751 24 Uppsala, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Federica","family":"Di Palma","sequence":"additional","affiliation":[{"name":"1 Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, 2 School of Engineering and Applied Sciences, Harvard University, 33 Oxford Street, Cambridge, MA 02138, USA and 3 Department of Medical Biochemistry and Microbiology, Uppsala University, Box 597, SE-751 24 Uppsala, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kerstin","family":"Lindblad-Toh","sequence":"additional","affiliation":[{"name":"1 Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, 2 School of Engineering and Applied Sciences, Harvard University, 33 Oxford Street, Cambridge, MA 02138, USA and 3 Department of Medical Biochemistry and Microbiology, Uppsala University, Box 597, SE-751 24 Uppsala, Sweden"},{"name":"1 Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, 2 School of Engineering and Applied Sciences, Harvard University, 33 Oxford Street, Cambridge, MA 02138, USA and 3 Department of Medical Biochemistry and Microbiology, Uppsala University, Box 597, SE-751 24 Uppsala, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2010,3,5]]},"reference":[{"key":"2023012508081449700_B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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