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MUMMER

swMATH ID: 17256
Software Authors: S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu, S.L. Salzberg
Description: MUMmer Ultra-fast alignment of large-scale DNA and protein sequences. MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences. The original MUMmer system, version 1.0, is described in our 1999 Nucleic Acids Research paper. Version 2.1 appeared a few years later and is described in our 2002 Nucleic Acids Research paper, while MUMmer 3.0 was recently described in our 2004 Genome Biology paper. We have also developed a GPU accelerated version of MUMmer called MUMmerGPU.
Homepage: http://mummer.sourceforge.net/
Related Software: LAGAN; REPuter; BLASTZ; PatternHunter; AVID; DIALIGN; BLAT; T-coffee; MUSCLE; PipMaker; ClustalW; MAFFT; BLAST; PSI-BLAST; LEDA; Velvet; Bio++; Cgaln; UniProt; bioperl
Cited in: 29 Publications

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