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 31 articles )

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  1. I, Tomohiro; Köppl, Dominik: Improved upper bounds on all maximal (\alpha)-gapped repeats and palindromes (2019)
  2. Rani, Seema; Rajpoot, Dharmveer Singh: Improvised divide and conquer approach for the LIS problem (2018)
  3. Ganguly, Arnab; Hon, Wing-Kai; Shah, Rahul; Thankachan, Sharma V.: Space-time trade-offs for finding shortest unique substrings and maximal unique matches (2017)
  4. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  5. Quiroz-Ibarra, J. Emilio; Mallén-Fullerton, Guillermo M.; Fernández-Anaya, Guillermo: DNA paired fragment assembly using graph theory (2017)
  6. Barsky, Marina; Stege, Ulrike; Thomo, Alex: Suffix trees for inputs larger than Main memory (2011) ioport
  7. Kirzhner, V.; Frenkel, S.; Korol, A.: Minimal-dot plot: “Old tale in new skin” about sequence comparison (2011) ioport
  8. Crochemore, Maxime; Porat, Ely: Fast computation of a longest increasing subsequence and application (2010)
  9. Elmasry, Amr: The longest almost-increasing subsequence (2010)
  10. Guyon, Frédéric; Brochier-Armanet, Céline; Guénoche, Alain: Comparison of alignment free string distances for complete genome phylogeny (2009)
  11. Althaus, Ernst; Canzar, Stefan: A Lagrangian relaxation approach for the multiple sequence alignment problem (2008)
  12. Christley, Scott; Lobo, Neil F.; Madey, Greg: Multiple organism algorithm for finding ultraconserved elements (2008) ioport
  13. Doring, Andreas; Weese, David; Rausch, Tobias; Reinert, Knut: Seqan - an efficient, generic C++ library for sequence analysis (2008) ioport
  14. Gao, Feng; Zaki, Mohammed J.: PSIST: a scalable approach to indexing protein structures using suffix trees (2008)
  15. Guyon, Frédéric; Guénoche, Alain: Comparing bacterial genomes from linear orders of patterns (2008)
  16. Albert, M. H.; Atkinson, M. D.; Nussbaum, Doron; Sack, Jörg-Rüdiger; Santoro, Nicola: On the longest increasing subsequence of a circular list (2007)
  17. Chan, Wun-Tat; Zhang, Yong; Fung, Stanley P. Y.; Ye, Deshi; Zhu, Hong: Efficient algorithms for finding a longest common increasing subsequence (2007)
  18. Schatz, Michael C.; Trapnell, Cole; Delcher, Arthur L.; Varshney, Amitabh: High-throughput sequence alignment using graphics processing units (2007) ioport
  19. Althaus, Ernst; Caprara, Alberto; Lenhof, Hans-Peter; Reinert, Knut: A branch-and-cut algorithm for multiple sequence alignment (2006)
  20. Joseph, Jijoy; Sasikumar, Roschen: Chaos game representation for comparison of whole genomes (2006) ioport

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