MUMMER

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.


References in zbMATH (referenced in 39 articles )

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  1. Geissmann, Barbara: Longest increasing subsequence under persistent comparison errors (2020)
  2. Lo, Shou-Fu; Tseng, Kuo-Tsung; Yang, Chang-Biau; Huang, Kuo-Si: A diagonal-based algorithm for the longest common increasing subsequence problem (2020)
  3. I, Tomohiro; Köppl, Dominik: Improved upper bounds on all maximal (\alpha)-gapped repeats and palindromes (2019)
  4. Rani, Seema; Rajpoot, Dharmveer Singh: Improvised divide and conquer approach for the LIS problem (2018)
  5. Ganguly, Arnab; Hon, Wing-Kai; Shah, Rahul; Thankachan, Sharma V.: Space-time trade-offs for finding shortest unique substrings and maximal unique matches (2017)
  6. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  7. Quiroz-Ibarra, J. Emilio; Mallén-Fullerton, Guillermo M.; Fernández-Anaya, Guillermo: DNA paired fragment assembly using graph theory (2017)
  8. Alam, Muhammad Rashed; Rahman, M. Sohel: A divide and conquer approach and a work-optimal parallel algorithm for the LIS problem (2013)
  9. Schirmer, Stefanie; Giegerich, Robert: Forest alignment with affine gaps and anchors, applied in RNA structure comparison (2013)
  10. Barsky, Marina; Stege, Ulrike; Thomo, Alex: Suffix trees for inputs larger than Main memory (2011) ioport
  11. Kirzhner, V.; Frenkel, S.; Korol, A.: Minimal-dot plot: “Old tale in new skin” about sequence comparison (2011) ioport
  12. Crochemore, Maxime; Porat, Ely: Fast computation of a longest increasing subsequence and application (2010)
  13. Elmasry, Amr: The longest almost-increasing subsequence (2010)
  14. Kryukov, Kirill; Saitou, Naruya: MISHIMA - a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data (2010) ioport
  15. Nakato, Ryuichiro; Gotoh, Osamu: Cgaln: fast and space-efficient whole-genome alignment (2010) ioport
  16. Wolfgruber, Thomas K.; Presting, Gernot G.: Junctionviewer: customizable annotation software for repeat-rich genomic regions (2010) ioport
  17. Guyon, Frédéric; Brochier-Armanet, Céline; Guénoche, Alain: Comparison of alignment free string distances for complete genome phylogeny (2009)
  18. Phillippy, Adam M.; Deng, Xiangyu; Zhang, Wei; Salzberg, Steven L.: Efficient oligonucleotide probe selection for pan-genomic tiling arrays (2009) ioport
  19. Althaus, Ernst; Canzar, Stefan: A Lagrangian relaxation approach for the multiple sequence alignment problem (2008)
  20. Christley, Scott; Lobo, Neil F.; Madey, Greg: Multiple organism algorithm for finding ultraconserved elements (2008) ioport

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