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MGR specifications

Information


Unique identifier OMICS_21807
Name MGR
Alternative names Multiple Genome Rearrangements, webMGR
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output data A phylogenic tree and a representation.
Output format Newick,ASCII
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Version 2.01
Stability No
Source code URL http://grimm.ucsd.edu/DIST/MGR-2.01.tar.gz
Maintained No

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Information


Unique identifier OMICS_21807
Name MGR
Alternative names Multiple Genome Rearrangements, webMGR
Interface Web user interface
Restrictions to use None
Input data A uni- or multi-chromosomal genome.
Output data A representation of the unrooted tree recovered with clickable edges to display the possible optimal rearrangement events via the GRIMM web server, a pairwise distance matrix of the input genome and offers clickable pairwise scenarios and a signed permutation of the input genome as well as the ancestors recovered.
Output format ASCII
Computer skills Basic
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Publications for Multiple Genome Rearrangements

MGR in pipelines

 (3)
2017
PMCID: 5399880
PMID: 28439458
DOI: 10.7717/peerj.3162

[…] str. n139 in comparison to other exiguobacterium species, nucleotide syntenic blocks were obtained with mauve version 2.3.1 (). syntenic block permutations were exported and used as input for mgr (). mgr was used to calculate the minimum number of rearrangements between the species analyzed, and to recover the rearrangement dendrogram. genoplotr () was used to plot the syntenic blocks […]

2016
PMCID: 4943181
PMID: 27269365
DOI: 10.1093/gbe/evw109

[…] we identified the syntenic block of genes between sciadopitys and cycas using mauve 2.3.1 (). the resulting matrix of syntenic blocks was utilized to estimate the minimal inversion steps with mgr 2.0.1 (). the plastome map of sciadopitys was drawn using circos 0.67 ()., primer pairs listed in supplementary table s1 (supplementary material online) were used to amplify dna fragments […]

2011
PMCID: 3143096
PMID: 21736755
DOI: 10.1186/1471-2156-12-60

[…] the ucsc genome browser liftover tool http://genome.ucsc.edu/hgliftover. grimm [] was used to infer the orientation of the loci in prairie vole linkage map via a comparison to the mouse genome. mgr [] was then applied to the four-way comparison between the marker order in prairie vole linkage map and the mouse, rat and human genomes to estimate the number and types of rearrangements […]


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MGR in publications

 (37)
PMCID: 5959919
PMID: 29777105
DOI: 10.1038/s41467-018-04256-y

[…] that genome evolution accompanies vestiges of massive genome rearrangements, such as translocations (tls), deletions, insertions, and copy number variations (cnvs)–. human cancer cells also undergo multiple genome rearrangements, analogous to those occurring during genome evolution and that might promote their acquisition of malignancy. it is postulated that the source of those rearrangements […]

PMCID: 5914054
PMID: 29688842
DOI: 10.1186/s12864-018-4663-4

[…] block size and gap threshold (a maximum distance between genes in a synteny block). synteny blocks obtained by grimm-synteny were visualized using genoplotr []. the multiple genome rearrangement (mgr) program [] was used to determine the number and types of rearrangements that caused the synteny block reshuffling among three species. to run the random model for synteny blocks, we obtained […]

PMCID: 5635614
PMID: 29081686
DOI: 10.2174/1389202918666170307120943

[…] usually employ genome evolutionary models and search for the exact ancestral genomes that minimizes the total distance or events over all edges of the given phylogeny. bpanalysis [], grappa [] and mgr [] are the pioneering studies of distance/event-based approaches. they reconstruct the ancestral genomes by finding the local median genomes. these methods have already encountered challenges […]

PMCID: 5430533
PMID: 28428552
DOI: 10.1038/s41598-017-01144-1

[…] of 98 genes from 15 ulvophycean chloroplast genomes. the branch lengths of this tree were computed on the tree topology inferred from the raxml analyses of the sequence data using the -t option of mgr v2.03. because mgr cannot handle duplicated genes, only one copy of the ir and of each duplicated gene was included in the matrix., group ii intron sequences were aligned manually on the basis […]

PMCID: 5381562
PMID: 28172771
DOI: 10.1093/gbe/evw271

[…] partial sequences (psbz–trnsuga spacer, trnsgga–rps4) of geranium palmatum, e . carvifolium, and monsonia speciosa (; ) were used as outgroup., the plastome rearrangement history was analyzed with mgr () under a linear and undirected model over the fixed ml topology. we first restricted this reconstruction to our pcr-screened regions, that is, psbz, trnsgga, rps4, rbcl, psai, rps18, rpl20, […]


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MGR institution(s)
Department of Mathematics, University of Southern California, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
MGR funding source(s)
Supported by grants from the National Sciences and Engineering Research Council of Canada.

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