GRIMM protocols

GRIMM specifications

Information


Unique identifier OMICS_21806
Name GRIMM
Alternative name Genome Rearrangements in Man and Mouse
Interface Web user interface
Restrictions to use None
Programming languages C, Perl
Computer skills Basic
Version 2.01
Stability Stable
Source code URL http://grimm.ucsd.edu/DIST/GRIMM-2.01.tar.gz
Maintained Yes

Additional information


http://grimm.ucsd.edu/GRIMM/grimm_instr.html

Information


Unique identifier OMICS_21806
Name GRIMM
Alternative name Genome Rearrangements in Man and Mouse
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Perl
Computer skills Basic
Version 2.01
Stability Stable
Source code URL http://grimm.ucsd.edu/DIST/GRIMM-2.01.tar.gz
Maintained Yes

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Additional information


http://grimm.ucsd.edu/GRIMM/grimm_instr.html

Publications for Genome Rearrangements in Man and Mouse

GRIMM IN pipelines

 (3)
2016
PMCID: 5630911
PMID: 27503298
DOI: 10.1093/gbe/evw190

[…] genomes. the gloeotilopsis mtdnas show slight differences in gene organization: nearly 90% of their conserved genes and free-standing orfs form four syntenic blocks (fig. 1) and as inferred by grimm analysis, only four reversals are required to convert gene order in one genome to that of the other. our comparison of g. planctonica and g. sarcinoidea mtdnas with their pseudendoclonium […]

2016
PMCID: 5630911
PMID: 27503298
DOI: 10.1093/gbe/evw190

[…] of g. planctonica and g. sarcinoidea mtdnas with their pseudendoclonium counterpart revealed seven and eight syntenic blocks (fig. 1), respectively, with 11 and 12 reversals inferred using grimm., gloeotilopsis planctonica mtdna contains ten group i introns, seven of which are present in cox1, as well as one group ii intron, whereas g. sarcinoidea mtdna contains five group i introns […]

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

[…] the human (genome assembly version hg19) and rat genomes (genome assembly version rn4) of those loci was also inferred using the ucsc genome browser liftover tool http://genome.ucsc.edu/hgliftover. grimm [22] was used to infer the orientation of the loci in prairie vole linkage map via a comparison to the mouse genome. mgr [23] was then applied to the four-way comparison between the marker […]

GRIMM institution(s)
Department of Computer Science and Engineering, University of California, San Diego, CA, USA

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