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DRIMust specifications

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Unique identifier OMICS_03829
Name DRIMust
Alternative name Discovering Rank Imbalanced Motifs using suffix trees
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Publications for Discovering Rank Imbalanced Motifs using suffix trees

DRIMust citations

 (9)
library_books

Identification and characterization of roles for Puf1 and Puf2 proteins in the yeast response to high calcium

2017
Sci Rep
PMCID: 5465220
PMID: 28596535
DOI: 10.1038/s41598-017-02873-z

[…] to determine whether the affected mrnas contain the rna sequence that is recognized by puf2 (dual uaau motif). no enrichment for this motif was found using the ame tool of the meme suit or the drimust tool. taken together, our analyses reveal that already after 45 min, the expression of mrnas that were not known to be bound by puf1 or puf2 changes. this may suggest that downstream effects […]

library_books

Dysregulated IER3 Expression is Associated with Enhanced Apoptosis in Titin Based Dilated Cardiomyopathy

2017
Int J Mol Sci
PMCID: 5412309
PMID: 28353642
DOI: 10.3390/ijms18040723

[…] tested. the ier3 binding motif was confirmed by chipmotifs [], suite for computational identification of promoter elements (scope) [] and discovering ranked imbalanced motifs using suffix trees (drimust) [] and then analyzed by find individual motif occurrences (fimo) [] for identification of potential ier3 targets. from the matches, two anti-apoptotic (akt1 and bcl2l1) and three […]

library_books

RNA protein binding motifs mining with a new hybrid deep learning based cross domain knowledge integration approach

2017
BMC Bioinformatics
PMCID: 5331642
PMID: 28245811
DOI: 10.1186/s12859-017-1561-8

[…] only using the sequence information. for instance, matrixreduce simply fits a statistical mechanical model to infer the sequence-specific binding sites for transcription factors from sequences []. drimust discovers motifs by integrating the minimum hyper-geometric statistical framework with suffix trees for fast enumerating motifs []., besides the high-throughput sequences, actually multiple […]

library_books

Regulation of alternative splicing at the single‐cell level

2015
Mol Syst Biol
PMCID: 4704489
PMID: 26712315
DOI: 10.15252/msb.20156278

[…] steps, 2,731 cassette exons were retained ()., to determine whether cassette exons with conserved firs are enriched in splicing factor binding motifs, we first searched for fir‐enriched k‐mers using drimust (leibovich et al, ), a tool for identifying short motifs in a ranked list of nucleic acid sequences. we performed this analysis independently for upstream and downstream fir sequences ranked […]

library_books

High throughput characterization of protein–RNA interactions

2014
Brief Funct Genomics
PMCID: 4303715
PMID: 25504152
DOI: 10.1093/bfgp/elu047

[…] algorithms that incorporate gapped positions have been developed [] but have not been extensively applied to rna–protein interaction data. exceptions include leibovich and yakhini, who applied the drimust algorithm to a rip-chip data set of yeast pum-hd proteins, several of which displayed gapped motifs [], and hidden markov model-based approaches for detecting clustered binding sites in ptb […]

library_books

Mutual enrichment in ranked lists and the statistical assessment of position weight matrix motifs

2014
PMCID: 4021615
PMID: 24708618
DOI: 10.1186/1748-7188-9-11

[…] expression data or of correlations computed between genomic dna copy number and expression [-]. fatigo [] is also a tool that is useful in the context of analysing go terms in ranked lists of genes. drimust [-] searches for sequence motifs that are enriched, in a statistically significant manner, in the top of a ranked list of sequences, which can be produced by techniques like chip-seq., […]


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DRIMust institution(s)
Department of Computer Science, Technion - Israel Institute of Technology, Technion City, Haifa, Israel; Department of Biology, Technion-Israel Institute of Technology, Technion City, Haifa, Israel; Agilent Laboratories Israel, Petach-Tikva, Israel
DRIMust funding source(s)
Supported by Niedersachsen-Israel Grant, Israel Ministry of Science and Technology and by ISEF Fellowship.

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