Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
, 5 (2), R12

Versatile and Open Software for Comparing Large Genomes

Comparative Study

Versatile and Open Software for Comparing Large Genomes

Stefan Kurtz et al. Genome Biol.


The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes. Two new graphical viewing tools provide alternative ways to analyze genome alignments. The new system is the first version of MUMmer to be released as open-source software. This allows other developers to contribute to the code base and freely redistribute the code. The MUMmer sources are available at


Figure 1
Figure 1
Dot-plot alignments of a 2.9 Mbp chromosome of A. fumigatus (x-axis) to a 2.1 Mbp scaffold of A. nidulans (y-axis). Left: nucleotide-based alignment with Nucmer. Right: amino-acid-based alignment with Promer. Aligned segments are represented as dots or lines, up to 3,000 bp long in the Nucmer alignment and up to 9,500 bp in the Promer alignment. These alignments were generated by the mummerplot script and the Unix program gnuplot.
Figure 2
Figure 2
Sample display from DisplayMUMs, showing whole-genome alignment of individual shotgun reads (query sequences) to a contig from the Staphylococcus epidermidis genome. The display illustrates how exact matches of the tiling reads can be seen against the contig consensus. Green and red colors in the query sequences indicate alignment on the forward and reverse strands, respectively.
Figure 3
Figure 3
Sample display created by the MapView program, showing a 185 kbp slice of D. melanogaster chromosome 2L and its alignment to D. pseudoobscura. The alignment, generated by Promer, shows all regions of conserved amino acid sequence. The blue rectangle spanning the figure represents the reference (D. melanogaster), with annotated genes shown above it. Alternative splice variants of the same gene are stacked vertically. Exons are shown as boxes, with intervening introns connecting them. The 5' and 3' UTRs are colored pink and blue to indicate the gene's direction of translation. Promer matches are shown twice, once just below the reference genome, where all matches are collapsed into red boxes, and in a larger display showing the separate matches within each contig, where the contigs are colored differently to indicate contig boundaries. The vertical position of the matches indicates their percent identity, ranging from 50% at the bottom of the display to 100% just below the red rectangles.

Similar articles

See all similar articles

Cited by 1,849 PubMed Central articles

See all "Cited by" articles


    1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–410. doi: 10.1006/jmbi.1990.9999. - DOI - PubMed
    1. Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA. 1988;85:2444–2448. - PMC - PubMed
    1. Alm RA, Ling LS, Moir DT, King BL, Brown ED, Doig PC, Smith DR, Noonan B, Guild BC, deJonge BL, et al. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature. 1999;397:176–80. doi: 10.1038/16495. - DOI - PubMed
    1. Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty BA, et al. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature. 1997;388:539–47. doi: 10.1038/41483. - DOI - PubMed
    1. Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL. Alignment of whole genomes. Nucleic Acids Res. 1999;27:2369–76. doi: 10.1093/nar/27.11.2369. - DOI - PMC - PubMed

Publication types

LinkOut - more resources