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.
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.
Mummer is a fast algorithm used for the rapid alignment of entire genomes. The MUMmer algorithm is relatively new and has 4 versions.
Versions of MUMmersedit
MUMmer1edit
MUMmer1 or just MUMmer consists of three parts, the first part consists of the creation of suffix trees (to get MUMs), the second part in the longest increasing subsequence or longest common subsequences (to order MUMs), lastly any alignment to close gaps.
Interruptions between MUMs-alignment, are known as gaps. Otherther alignment algorithms fill these gaps. The gaps fall in the following four classes:[4]
An SNPinterruption – when comparing two sequences, one character will differ.
An insertion – when comparing two sequences, there is a subsequence in only appears in one of the sequences. It would be an empty gap in the other sequence at the moment of comparison of the two sequences.
A highly polymorphic region – when comparing two sequences, there can be found a subsequence in which every single character differs.
A repeat – it’s the repetition of a sequence. Since MUMs can only take unique sequences, that gap can be one repetition of one of the MUMs.
MUMmer 2edit
This algorithm was redesigned to require less memory and increase speed and accuracy. It also allows for bigger genomes alignment.
The improvement was the amount stored in the suffix trees by employing the one created by Kurtz.
MUMmer 3edit
According to Stefan Kurtz and his teammates, “the most significant technical improvement in MUMmer 3.0, is a complete rewrite of the suffix-tree code, based on the compact suffix- tree representation of” [5] the tree described in the article “Reducing the space requirement of suffix trees”.[6]
MUMmer 4edit
According to Guillaume and his team, there are some extra improvements in the implementation and also innovation with Query parallelism. “MUMmer4 now includes options to save and load the suffix array for a given reference."[7] This allows the suffix tree can be built once and constructed again after running it from the saved suffix tree.
^Kurtz, S.; Phillippy, A.; Delcher, A.; Smoot, M.; Shumway, M.; Antonescu, C.; Salzberg, S. (2004). "Versatile and open software for comparing large genomes" (PDF). Genome Biology. 5 (2): R12. doi:10.1186/gb-2004-5-2-r12. PMC395750. PMID 14759262. (PDF) from the original on 2019-07-11. Retrieved 2021-05-06.
^Kurtz, S. (1999). "Reducing the Space Requirement of Suffix Trees". Software: Practice and Experience. 29 (13): 1149–1171. doi:10.1002/(SICI)1097-024X(199911)29:13<1149::AID-SPE274>3.0.CO;2-O. from the original on 2021-05-06. Retrieved 2021-05-06.
^Marçais, Guillaume.; Pillippy, A.; Delcher, A.; Coston, R.; Salzberg, S.; Zimin, A. (2018). "MUMmer4: A fast and versatile genome alignment system". PLOS Computational Biology. 14 (1): e1005944. Bibcode:2018PLSCB..14E5944M. doi:10.1371/journal.pcbi.1005944. PMC5802927. PMID 29373581.
External linksedit
MUMmer home page
MUMmer2
Book
MUMmer
Software
MUMmer3
MUMmer1
MUMmer4
April 10, 2024
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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 Contents 1 Overview 2 Versions of MUMmers 2 1 MUMmer1 2 2 MUMmer 2 2 3 MUMmer 3 2 4 MUMmer 4 3 Software Open Source 4 Related Sequence Alignments 5 References 6 External linksOverview editMummer is a fast algorithm used for the rapid alignment of entire genomes The MUMmer algorithm is relatively new and has 4 versions Versions of MUMmers editMUMmer1 edit MUMmer1 or just MUMmer consists of three parts the first part consists of the creation of suffix trees to get MUMs the second part in the longest increasing subsequence or longest common subsequences to order MUMs lastly any alignment to close gaps Interruptions between MUMs alignment are known as gaps Otherther alignment algorithms fill these gaps The gaps fall in the following four classes 4 An SNPinterruption when comparing two sequences one character will differ An insertion when comparing two sequences there is a subsequence in only appears in one of the sequences It would be an empty gap in the other sequence at the moment of comparison of the two sequences A highly polymorphic region when comparing two sequences there can be found a subsequence in which every single character differs A repeat it s the repetition of a sequence Since MUMs can only take unique sequences that gap can be one repetition of one of the MUMs MUMmer 2 edit This algorithm was redesigned to require less memory and increase speed and accuracy It also allows for bigger genomes alignment The improvement was the amount stored in the suffix trees by employing the one created by Kurtz MUMmer 3 edit According to Stefan Kurtz and his teammates the most significant technical improvement in MUMmer 3 0 is a complete rewrite of the suffix tree code based on the compact suffix tree representation of 5 the tree described in the article Reducing the space requirement of suffix trees 6 MUMmer 4 edit According to Guillaume and his team there are some extra improvements in the implementation and also innovation with Query parallelism MUMmer4 now includes options to save and load the suffix array for a given reference 7 This allows the suffix tree can be built once and constructed again after running it from the saved suffix tree Software Open Source editMUMmer has open source software and can be accessed online Related Sequence Alignments editThere are other types of sequence alignments Edit distance BLAST Bowtie BWA Blat Mauve LASTZ BLASTReferences edit 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 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 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 Delcher A Kasif S Fleischmann R Peterson J White O Salzberg S 1999 Alignment of Whole Genomes Nucleic Acids Research 27 11 2369 2376 doi 10 1093 nar 27 23 4636 PMC 148804 PMID 10325427 Kurtz S Phillippy A Delcher A Smoot M Shumway M Antonescu C Salzberg S 2004 Versatile and open software for comparing large genomes PDF Genome Biology 5 2 R12 doi 10 1186 gb 2004 5 2 r12 PMC 395750 PMID 14759262 Archived PDF from the original on 2019 07 11 Retrieved 2021 05 06 Kurtz S 1999 Reducing the Space Requirement of Suffix Trees Software Practice and Experience 29 13 1149 1171 doi 10 1002 SICI 1097 024X 199911 29 13 lt 1149 AID SPE274 gt 3 0 CO 2 O Archived from the original on 2021 05 06 Retrieved 2021 05 06 Marcais Guillaume Pillippy A Delcher A Coston R Salzberg S Zimin A 2018 MUMmer4 A fast and versatile genome alignment system PLOS Computational Biology 14 1 e1005944 Bibcode 2018PLSCB 14E5944M doi 10 1371 journal pcbi 1005944 PMC 5802927 PMID 29373581 External links editMUMmer home page MUMmer2 Book MUMmer Software MUMmer3 MUMmer1 MUMmer4 Retrieved from https en wikipedia org w index php title MUMmer amp oldid 1197786171, wikipedia, wiki, book, books, library,
