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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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Additional information


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

Publications for Genome Rearrangements in Man and Mouse

GRIMM citations

 (50)
library_books

Partial arm translocations in evolution of malaria mosquitoes revealed by high coverage physical mapping of the Anopheles atroparvus genome

2018
BMC Genomics
PMCID: 5914054
PMID: 29688842
DOI: 10.1186/s12864-018-4663-4

[…] es 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 $ 7 8 […]

library_books

Rapid emergence of independent “chromosomal lineages” in silvered leaf monkey triggered by Y/autosome translocation

2018
Sci Rep
PMCID: 5818525
PMID: 29459623
DOI: 10.1038/s41598-018-21509-4

[…] in the CGU2 chromosomal form, generating the LCA form. We carefully considered if the LCA form was actually the last common form with respect to TCR1a, TCR1b, Y1, and Y2. We examined, exploiting the GRIMM software, the potential different forms generated by the inversions when introduced in different chronologies, but no alternatives were found. We also considered the possibility that Y1 and Y2 c […]

call_split

Comparative physical genome mapping of malaria vectors Anopheles sinensis and Anopheles gambiae

2017
Malar J
PMCID: 5460330
PMID: 28583133
DOI: 10.1186/s12936-017-1888-7
call_split See protocol

[…] e number of all synteny blocks, the inversion distances on homologous chromosome arms between An. sinensis and An. gambiae were estimated using the programs of Genome Rearrangements in Mouse and Man (GRIMM) []. […]

library_books

Large Scale Comparative Analysis Reveals the Mechanisms Driving Plastomic Compaction, Reduction, and Inversions in Conifers II (Cupressophytes)

2016
Genome Biol Evol
PMCID: 5491842
PMID: 28039231
DOI: 10.1093/gbe/evw278

[…] 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. […]

library_books

Mitochondrion to Chloroplast DNA Transfers and Intragenomic Proliferation of Chloroplast Group II Introns in Gloeotilopsis Green Algae (Ulotrichales, Ulvophyceae)

2016
Genome Biol Evol
PMCID: 5630911
PMID: 27503298
DOI: 10.1093/gbe/evw190

[…] repertoire, which only differs from that of Pseudendoclonium by the absence of trnR(ccu) (B), comprises 104 different conserved genes coding for 73 proteins, three rRNAs and 28 tRNAs. As revealed by GRIMM analyses, seven reversals account for the alterations in gene order between the two Gloeotilopsis cpDNAs; 101 of their 104 shared conserved genes form six syntenic blocks, with the longest conta […]

call_split

Comparative Chloroplast Genome Analyses of Streptophyte Green Algae Uncover Major Structural Alterations in the Klebsormidiophyceae, Coleochaetophyceae and Zygnematophyceae

2016
Front Plant Sci
PMCID: 4877394
PMID: 27252715
DOI: 10.3389/fpls.2016.00697
call_split See protocol

[…] Syntenic regions in pairwise genome comparisons were identified using a custom-built program and the number of gene reversals between the compared genomes was estimated with GRIMM v2.01 (). The same custom-built program was employed to convert gene order to all possible pairs of signed genes (i.e., taking into account gene polarity); the gene pairs conserved in three or m […]

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

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