MUMmer

MUMmer is a bioinformatics software system for sequence alignment. It is based on the suffix tree data structure. It has been used for comparing different genomes assemblies to one another, which allows scientists to determine how a genome has changed. 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 the comparison of two related strains of bacteria.

The MUMmer software is open source. 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)[1] has been cited 691 times; the MUMmer 2 paper (Delcher et al., 2002)[2] has been cited 455 times; and the MUMmer 3.0 article (Kurtz et al., 2004)[3] has been cited 903 times.

  1. ^ 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.
  2. ^ 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.
  3. ^ 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.