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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 citations

 (6)
library_books

A gene expression study of dorso ventrally restricted pigment pattern in adult fins of Neolamprologus meeli, an African cichlid species

2017
PeerJ
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 matric […]

library_books

Anterior posterior gene expression differences in three Lake Malawi cichlid fishes with variation in body stripe orientation

2017
PeerJ
PMCID: 5695249
PMID: 29158996
DOI: 10.7717/peerj.4080

[…] ssing 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 ma […]

library_books

RNA dependent chromatin association of transcription elongation factors and Pol II CTD kinases

2017
eLife
PMCID: 5457138
PMID: 28537551
DOI: 10.7554/eLife.25637.021

[…] ional 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. CU […]

library_books

Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences

2016
Nucleic Acids Res
PMCID: 5291271
PMID: 27288444
DOI: 10.1093/nar/gkw521

[…] ent method to estimate the biological significance of discovered motifs, and (iv) introduce positional priors. (v) Since BaMM!motif's speed is at present limited by the seed motif discovery code from XXmotif, we will accelerate this code substantially. One future challenge will also be (vi) to develop a rigorous approach that can deal with quantitative data such as fluorescence intensities from HT […]

library_books

RECQL5 Controls Transcript Elongation and Suppresses Genome Instability Associated with Transcription Stress

2014
Cell
PMCID: 4032574
PMID: 24836610
DOI: 10.1016/j.cell.2014.03.048

[…] an across each interval for all peaks was taken and plotted. Characterization of Transcription Stress Sequence Features/Signatures Overrepresented sequence consensus elements were searched for with XXmotif () (settings:–zoops–type ALL–localization–merge-motif-threshold LOW) in ±50 and ±400 bps surrounding RNAPII peaks occurring in the transcribed regions, excluding the first 500 bp of genes (to […]

library_books

TGF β stimulation in human and murine cells reveals commonly affected biological processes and pathways at transcription level

2014
BMC Syst Biol
PMCID: 4049504
PMID: 24886091
DOI: 10.1186/1752-0509-8-55

[…] BSs) was performed using the de novo sequence motif detection method XXmotifs []. Identified sequence motifs were then aligned to known TRANSFAC TFBS via STAMP [] and the top match is considered. The XXmotif method uses BLAST [] all-against-all comparisons to mask regions of local homology in order to avoid false positives. The method then performs an enrichment analysis after transforming the fou […]

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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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