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DRIMust specifications

Information


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 in pipeline

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

[…] splicing sequences were predicted with sroogle (schwartz et al, ) and removed from the inspected fir sequences. next, we computed the similarity of all the significantly enriched k‐mers reported by drimust (false discovery rate (fdr)‐corrected (benjamini & hochberg, ) p < 0.05 in both cassette exon groups) to a list of motifs of known splicing factors (cook et al, ; ray et al, ) ( and ), […]


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DRIMust in publications

 (9)
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 […]

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 […]

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 […]

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 […]

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 […]


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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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