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CompariMotif specifications

Information


Unique identifier OMICS_07749
Name CompariMotif
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 2.0
Computer skills Advanced
Version 3.11
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Denis Shields

Information


Unique identifier OMICS_07749
Name CompariMotif
Interface Web user interface
Restrictions to use Academic or non-commercial use
Programming languages Python
Computer skills Basic
Version 3.11
Stability Stable
Maintained Yes

Maintainer


  • person_outline Denis Shields

Publication for CompariMotif

CompariMotif citations

 (12)
library_books

Synergy: A Web Resource for Exploring Gene Regulation in Synechocystis sp. PCC6803

2014
PLoS One
PMCID: 4242644
PMID: 25420108
DOI: 10.1371/journal.pone.0113496

[…] he phylogenetic footprinting approach resulted in many motifs that were similar to each other. To eliminate duplicates, a motif similarity network was constructed. The similarities were calculated by CompariMotif using the consensus motifs derived from the position specific scoring matrices (PSSMs) as input. The motif network was then clustered using MCL . The motif with the highest betweenness c […]

library_books

Quantitative phosphoproteomic profiling of fiber differentiation and initiation in a fiberless mutant of cotton

2014
BMC Genomics
PMCID: 4070576
PMID: 24923550
DOI: 10.1186/1471-2164-15-466

[…] r pTyr, less stringent settings of width = 13, occurrence = 2, and significance = 0.0005 were used because only 18 peptides contained localized pTyr motifs. Motif identification was carried out using CompariMotif [] and the PhosphoMotif Finder database []. Phosphoproteins and phosphor-13-mer sequences were compared against the P3DB database (9 species, 16,477 phosphoproteins, and 47,923 phosphosit […]

call_split

Potential of known and short prokaryotic protein motifs as a basis for novel peptide based antibacterial therapeutics: a computational survey

2014
Front Microbiol
PMCID: 3896991
PMID: 24478765
DOI: 10.3389/fmicb.2014.00004
call_split See protocol

[…] n datasets sequences longer than 40 amino acids prior to the analysis.The motifs identified by the SLiMFinder analysis were further examined for similarity to known SLiMs from literature motifs using CompariMotif, which takes two lists of protein motifs and compares them to each other, identifying and scoring similarities between short motifs in the sets (Edwards et al., ).Motifs were visualized u […]

library_books

A Computational Systems Biology Study for Understanding Salt Tolerance Mechanism in Rice

2013
PLoS One
PMCID: 3676415
PMID: 23762267
DOI: 10.1371/journal.pone.0064929

[…] a Chi-squared test on the significance of these motifs in comparison to randomly selected genes in the genome. We compared the identified motifs with known plant motifs from the PLACE database using CompariMotif . For each pair of compared motifs, if their similarity score is more than 4 and the percentage of their matched positions is more than 80%, these two motifs were considered identical. […]

library_books

Protein Disorder and Short Conserved Motifs in Disordered Regions Are Enriched near the Cytoplasmic Side of Single Pass Transmembrane Proteins

2012
PLoS One
PMCID: 3433447
PMID: 22962613
DOI: 10.1371/journal.pone.0044389

[…] olutionary change in the flanks over shorter evolutionary spans to provide a signal to detect motifs.Other motifs bear partial or striking similarity to known motifs (), which we identified using the CompariMotif program , drawing on known motif databases including ELM and MiniMotif . For instance the motif predicted on the juxtamembrane region of low-density lipoprotein receptor-related protein […]

library_books

Genome scale identification of cell wall related genes in Arabidopsis based on co expression network analysis

2012
BMC Plant Biol
PMCID: 3463447
PMID: 22877077
DOI: 10.1186/1471-2229-12-138

[…] hat for the Rice genome, a 5’ un-translated region could be as long as 3,000 bps while for Populus, its 5’ un-translated region is no more than 1,000 bps (Additional file : Figure S3b-c).We have used CompariMotif [] to integrate all the predicted motifs by the three programs, particularly highly similar predictions among the co-expression modules. Specifically, a similarity score for each pair of […]

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CompariMotif institution(s)
UCD Complex and Adaptive Systems Laboratory, University College Dublin, Dublin

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