ArticleBioinformatics (Oxford, England)2010
Genome-wide synteny through highly sensitive sequence alignment: Satsuma.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 168 papers.
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Who cites it
168 citing papers in PubMed.
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- MGA: a tool for haplotype-mixed assembly of long and accurate reads.Genome biology · 2026Article
- First high-density linkage map based on GBS derived genome wide SNP markers in Labeo catla (Hamilton, 1822).Scientific data · 2026Article
- Tracing the Drivers of Range-Wide Bowhead Whale Genomic Structure and Diversity.Molecular ecology · 2026Article
- Unique sex chromosome translocations and evolutionary strata in two Sylvioidea songbird families.BMC genomics · 2026Article
- Strain, procedures, and tools for reproducible genetic transformation and genome editing of the emerging plant model Spirodela polyrhiza.The New phytologist · 2026Article
- Comparative analysis of venom genes in the chromosome-level genomes of two closely related cone snails.BMC genomics · 2026Article
- A chromosome-scale genome assembly of the striped fruit fly Zeugodacus scutellatus (Diptera: Tephritidae).Scientific data · 2026Article
- Pleistocene demographic histories dominate contemporary genomic diversity in a continental radiation of Himalayan-Hengduan songbirds.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The evolutionary history of the field vole species complex revealed by modern and ancient genomes.Genome biology · 2026Article
- Major changes in gene expression between strains of diapausing and non-diapause spruce budworm.PloS one · 2026Article
- ntSynt: multi-genome synteny detection using minimizer graph mappings.BMC biology · 2025Article
- Palaeogenomics suggest domesticated camelid herding and wild camelid hunting in early pastoralist societies in the Atacama Desert.Nature communications · 2025Article
- Genomic Signatures and Demographic History of the Widespread and Critically Endangered Yellow-Breasted Bunting.Molecular ecology · 2025Article
- Life inside a bag: multiomics insights into the bagworm species Eumeta crameri.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Speciation Genomics in the Tiger Whiptail Lizards (Aspidoscelis tigris Complex).Genome biology and evolution · 2025Article
108 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
motivationComparative 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).
resultsSatsuma 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/.
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Registered trials
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