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MUMmer is a bioinformatics software system for sequence alignment. It is based on the suffix tree data structure and is one of the fastest and most efficient systems available for this task, enabling it to be applied to very long sequences. It has been widely used for comparing different genomes to one another. In recent years it has become a popular algorithm for comparing genome assemblies to one another, which allows scientists to determine how a genome has changed after adding more DNA sequence or after running a different genome assembly program. The acronym "MUMmer" comes from "Maximal Unique Matches", or MUMs. The original algorithms in the MUMMER software package were designed by Art Delcher, Simon Kasif and Steven Salzberg. Mummer was the first whole genome comparison system developed in Bioinformatics. It was originally applied to comparison of two related strains of bacteria.
The MUMmer software is open source and can be found at the MUMmer home page. The home page also has links to technical papers describing the system. The system is maintained primarily by Steven Salzberg and Arthur Delcher at Center for Computational Biology at Johns Hopkins University.
MUMmer is a highly cited bioinformatics system in the scientific literature. According to Google Scholar, as of early 2013 the original MUMmer paper (Delcher et al., 1999) has been cited 691 times; the MUMmer 2 paper (Delcher et al., 2002) has been cited 455 times; and the MUMmer 3.0 article (Kurtz et al., 2004) has been cited 903 times.
- Delcher, A. L.; Kasif, S.; Fleischmann, R. D.; Peterson, J.; White, O.; Salzberg, S. L. (1999). "Alignment of whole genomes". Nucleic acids research 27 (11): 2369–2376. doi:10.1093/nar/27.11.2369. PMC 148804. PMID 10325427.
- Delcher, A. L.; Phillippy, A.; Carlton, J.; Salzberg, S. L. (2002). "Fast algorithms for large-scale genome alignment and comparison". Nucleic acids research 30 (11): 2478–2483. doi:10.1093/nar/30.11.2478. PMC 117189. PMID 12034836.
- Delcher, A.; Harmon, D.; Kasif, S.; White, O.; Salzberg, S. (1999). "Improved microbial gene identification with GLIMMER". Nucleic Acids Research 27 (23): 4636–4641. doi:10.1093/nar/27.23.4636. PMC 148753. PMID 10556321.