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XXmotif specifications

Information


Unique identifier OMICS_06267
Name XXmotif
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for XXmotif

XXmotif in publications

 (13)
PMCID: 5637254
PMID: 29020934
DOI: 10.1186/s12864-017-4183-7

[…] or near sites of sr45-dependent alternative splicing., first, we submitted the plus (mrna-like) strand of all reads from the 1812 sar genes identified by both of our analysis pipelines (fig. ) to xxmotif []. significant motifs from this analysis (over-represented relative to expectation based on nucleotide frequencies) that were not also enriched in the control were related to ggnggngg, […]

PMCID: 5886188
PMID: 28335003
DOI: 10.1093/hmg/ddx092

[…] are provided in the ., full motif analysis steps are documented in the . briefly, we carried out de novo motif analysis using multiple parallel approaches: meme-chip () from the meme suite (), xxmotif () and pscanchip () from the weeder/modtools suite (). for the meme-chip and xxmotif analyses, we used the peak intervals in cpo10 and extracted the sequence underlying each interval ± 150bp […]

PMCID: 5228514
PMID: 28097057
DOI: 10.7717/peerj.2843

[…] performed motif enrichment analysis on 1 kb promoter sequences of two differentially expressed genes, based on the annotated genome of the nile tilapia () using three programs: meme (), scope () and xxmotif (). we retained the enriched motifs that were present in both promoters and screened for potential transcription factor (tf) binding sites using stamp (), with the motif position weight […]

PMCID: 5695249
PMID: 29158996
DOI: 10.7717/peerj.4080

[…] 2 kb upstream of the transcription starting sites of interesting genes emerging from the previous steps, using the annotated genome of the nile tilapia () as well as two algorithms: meme () and xxmotif (). we proceeded with the motifs that were enriched in the tested promoters and screened for potential transcription factor (tf) binding sites through stamp () and the motif position weight […]

PMCID: 5457138
PMID: 28537551
DOI: 10.7554/eLife.25637.021

[…] promoters producing cuts and mrnas of similar lengths ()., how can some efs distinguish between cuts and mrnas? we carried out motif analysis around the strongest par-clip sites for each ef using xxmotif () and could not find any significantly enriched motifs, indicating that efs bind rna in a non-specific manner. we hypothesize that another rna-binding factor blocks binding of efs to cuts. […]


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XXmotif institution(s)
Gene Center, Department of Biochemistry, and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität (LMU) München, Munich, Germany

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