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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

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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 in publications

 (8)
PMCID: 4070576
PMID: 24923550
DOI: 10.1186/1471-2164-15-466

[…] 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 […]

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

[…] 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 […]

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

[…] 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 […]

PMCID: 3463447
PMID: 22877077
DOI: 10.1186/1471-2229-12-138

[…] 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 […]

PMCID: 3421446
PMID: 22806145
DOI: 10.1038/msb.2012.31

[…] for every set of proteins with a particular pair of co-evolving ptms using the slimfinder () software. default parameters were used for this analysis. the extracted linear motifs were compared using comparimotif () software to known motifs belonging to all databases available in slimfinder., we performed a functional enrichment analysis with the proteins having crosstalking methylated […]


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

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