Alignment of whole genomes
Open accessAbstract
A new system for aligning whole genome sequences is described. Using an efficient data structure called a suffix tree, the system is able to rapidly align sequences containing millions of nucleotides. Its use is demonstrated on two strains of Mycoplasma tuberculosis, on two less similar species of Mycoplasma bacteria and on two syntenic sequences from human chromosome 12 and mouse chromosome 6. In each case it found an alignment of the input sequences, using between 30 s and 2 min of computation time. From the system output, information on single nucleotide changes, translocations and homologous genes can easily be extracted. Use of the algorithm should facilitate analysis of syntenic chromosomal regions, strain-to-strain comparisons, evolutionary comparisons and genomic duplications.
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The main idea of the MUMmer algorithm is to find all distinct matches for two given genomes.
“The main idea of this algorithm is to find all distinct matches for two given genomes [17].”
From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [17]
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Whole-Genome Alignment: Methods, Challenges, and Future Directions
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- Authors
- Delcher, A. L., Kasif, S., Fleischmann, R. D., Peterson, J., White, O., & Salzberg, S. L.
- Affiliations
- Loyola University Maryland (US)
- University of Illinois Chicago (US)
- Corresponding author
- Salzberg, S. L.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 1999-01-01
- Volume
- 27
- Issue
- 11
- Pages
- 2369-2376
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC148804
- OpenAlex
- W2152331922
- Cited by
- 893
- References
- 5
- Citations by year
- 2026: 8 · 2025: 11 · 2024: 20 · 2023: 22 · 2022: 32 · 2021: 21 · 2020: 41 · 2019: 37 · 2018: 39 · 2017: 22 · 2016: 29 · 2015: 23 · 2014: 20 · 2013: 30 · 2012: 21
- FWCI
- 9.66
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (9529227, 9530462)
- National Institutes of Health
- National Human Genome Research Institute (K01HG000022, K01-HG00022-1)
- National Institute of Allergy and Infectious Diseases (R01 AI40125-01, R01AI040125)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- whole-genome alignment, suffix trees, sequence alignment, Mycoplasma, strain comparison, translocation, homologous genes, genomic duplication, human chromosome 12, mouse chromosome 6
- MeSH terms
- Algorithms, Animals, Base Sequence, DNA, Humans, Molecular Sequence Data, Mycoplasma, Sequence Alignment, Genome, Bacterial, Mice
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