GRIMM protocols

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

Publications for Genome Rearrangements in Man and Mouse

GRIMM in pipelines

 (7)
2016
PMCID: 4743939
PMID: 26849226
DOI: 10.1371/journal.pone.0148934

[…] the tetraselmis and scherffelia chloroplast genomes were aligned using mauve 2.3.1 [] after removal of one copy of the ir. the number of reversals separating these genomes was estimated with grimm 2.01 []. we used a custom-built script to identify the regions that display the same gene order in the two chlorodendrophycean genomes. this perl script employs a concatenated list of signed […]

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 () 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 […]

2014
PMCID: 4169464
PMID: 25233465
DOI: 10.1371/journal.pone.0107854

[…] genbank using accession numbers kj958479 – kj958485. genome rearrangements were estimated with mauve after eliminating one copy of the inverted repeat . numbers of genome inversions were inferred by grimm ., genes absent from plastid genomes were searched for by blast searches in cyclotella nana nuclear genome against assembled contigs of transcriptome assemblies of t. weissflogii (mmetsp0878) […]

2012
PMCID: 3355041
PMID: 22296923
DOI: 10.1186/1471-2164-13-53

[…] as the distance from the final marker in one syntenic segment to the initial marker in the next syntenic segment. the two breakpoints belonging to the same inversion were associated with the aid of grimm results. once the two breakpoints of each inversion were identified, we proceeded to confirm these results by comparing the breakpoint regions sequences with d. virilis genome using flybase […]

2011
PMCID: 3037004
PMID: 21304168
DOI: 10.1128/mBio.00334-10

[…] phage isolate. homologous regions were aligned using clustalw (http://www.ebi.ac.uk/tools/msa/clustalw2/). we determined the dn, ds, and dn/ds () for every pair and the average values for each orf., grimm () found no major rearrangements between the progenitor phage and the respective related isolates. every aligned orf found above that was present in every phage was concatenated […]


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GRIMM in publications

 (51)
PMCID: 5914054
PMID: 29688842
DOI: 10.1186/s12864-018-4663-4

[…] indicating inter-arm rearrangements (fig. ). we calculated the numbers and determined types of rearrangements between chromosome elements using the mgr program [], which uses the same algorithm as grimm. the following orders and orientations of conserved blocks were used as an input for the mgr run, where the symbol $ indicates the end of each chromosome element.>an. gambiae1 $ 2 3 4 5 6 $ […]

PMCID: 5818525
PMID: 29459623
DOI: 10.1038/s41598-018-21509-4

[…] block organization of tcr1a/b, y1, y2, cgu2, and sen3 chromosomes in order to reconstruct a comprehensive evolutionary history of these chromosomes. the reconstruction was aided by the use of the grimm software, available online at http://grimm.ucsd.edu/grimm., the hypothesized evolutionary history of these chromosomes is graphically summarized in fig. . cca4 was used as the starting point. […]

PMCID: 5460330
PMID: 28583133
DOI: 10.1186/s12936-017-1888-7

[…] synteny blocks than the autosomes.fig. 3 table 4 , to further analyse fixed inversions between an. sinensis and an. gambiae, we input the order of 361 synteny blocks (additional file ) into the genome rearrangements in man and mouse (grimm) program []. table  shows that a minimum of 267 inversions were estimated between an. sinensis and an. gambiae. the sex chromosome exhibited a greater […]

PMCID: 5378121
PMID: 28188144
DOI: 10.1534/genetics.116.196154

[…] in both genomes with the total number of shared orthologs, and (ii) as the number of inversions separating the two genomes normalized by the number of shared orthologs. for the latter, we used the grimm version 2.01 program () to calculate the number of steps of the most parsimonious scenario transforming one genome into another by inversions. the dependence of rearrangement distance […]

PMCID: 5491842
PMID: 28039231
DOI: 10.1093/gbe/evw278

[…] ). lcbs shared by all examined taxa were collected to generate a matrix of lcb order., ancestral plastomes were inferred by using mlgo () with the ml tree and the lcb matrix mentioned above. we used grimm () to calculate the optimal number of inversions between plastomes., we used circos 0.67 () to draw plastome maps with their relative lcb orders. for the lcbs in inferred ancestral plastomes, […]


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

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