Genome-wide synteny through highly sensitive sequence alignment: Satsuma
Open accessAbstract
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
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The alignment-based method SatsumaSynteny2 takes pairs of genome sequences as input and implements a dynamic programming algorithm for chaining the pairwise alignment blocks.
“The alignment-based method SatsumaSynteny2 takes pairs of genome sequences as input and implements a dynamic programming algorithm for chaining the pairwise alignment blocks.”
From halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments (2020) · cites this paper as [5]
The Introduction (p. 1) describes Satsuma comparing query and target genomic sequences, and the Synteny filter (p. 3) says it uses dynamic programming to chain alignment matches. The paper describes Satsuma, however, not a method named SatsumaSynteny2, so it does not establish that the named method has these features. (LLM, conf=0.86)
Experimental — accuracy not yet measuredThe results of SatsumaSynteny2 in terms of genome coverage are similar to the ones reported by the benchmark study for the older version of SatsumaSynteny.
“The results of SatsumaSynteny2 in terms of genome coverage are similar to the ones reported by the benchmark study [14] for the older version of the tool SatsumaSynteny [5].”
From halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments (2020) · cites this paper as [5]
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Bellman, R. E. (2010) · doi:10.1515/9781400835386 · Cited by 14,588 · see citing works
An algorithm for the machine calculation of complex Fourier series
Cooley, J. W., & Tukey, J. W. (1965) · Mathematics of Computation · doi:10.1090/s0025-5718-1965-0178586-1 · Cited by 13,154 · see citing works
Genome sequence, comparative analysis and haplotype structure of the domestic dog
members, B. S. P., Lindblad-Toh, K., Wade, C. M., Mikkelsen, T. S., Karlsson, E. K., Jaffe, D. B., Kamal, M., Clamp, M., Chang, J. L., Kulbokas, E. J., et al. (2005) · Nature · doi:10.1038/nature04338 · Cited by 2,568 · see citing works
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Research works printed but not linked: 4
- Brodzik,A.K. (2005)Acomparative study of cross-correlation methods for alignment of DNAsequences containing repetitive patterns. In 13th European Signal Processing Conference EU-SIPCO 2005 . Available at http://www.eurasip.org/Proceedings/ Eusipco/Eusipco2005/defevent/papers/cr1487.pdf
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Krasheninnikova, K., Diekhans, M., Armstrong, J., Dievskii, A., Paten, B., & O'Brien, S. (2020) · GigaScience · doi:10.1093/gigascience/giaa047 · Cited by 30 · see citing works
- Authors
- Grabherr, M. G., Russell, P., Meyer, M., Mauceli, E., Alföldi, J., Di Palma, F., & Lindblad-Toh, K.
- Affiliations
- Broad Institute (US)
- 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
- Corresponding author
- Grabherr, Manfred G.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-03-05
- Volume
- 26
- Issue
- 9
- Pages
- 1145-1151
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC2859124
- OpenAlex
- W2109809376
- Cited by
- 287
- References
- 3
- Citations by year
- 2026: 27 · 2025: 31 · 2024: 30 · 2023: 21 · 2022: 28 · 2021: 33 · 2020: 29 · 2019: 24 · 2018: 17 · 2017: 14 · 2016: 7 · 2015: 7 · 2014: 9 · 2013: 2 · 2012: 1
- FWCI
- 1.21
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Bioinformatics (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Human Genome Research Institute (U54HG003067)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- comparative genomics, sequence alignment, cross correlation function, fast Fourier transform, match scoring, parallel alignment, vertebrate genomes, fish genomes
- MeSH terms
- Algorithms, Animals, Fourier Analysis, Humans, Probability, Programming Languages, Oryza, Software, Models, Statistical, Sequence Alignment, Genome, Computational Biology, Genomics, Tetraodontiformes, Sorghum
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