jPREdictor: a versatile tool for the prediction of cis-regulatory elements

Fiedler T, Rehmsmeier M (2006)
Nucleic Acids Research 34(Web Server): W546-W550.

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Gene regulation is the process through which an organism effects spatial and temporal differences in gene expression levels. Knowledge of cis-regulatory elements as key players in gene regulation is indispensable for the understanding of the latter and of the development of organisms. Here we present the tool jPREdictor for the fast and versatile prediction of cis-regulatory elements on a genome-wide scale. The prediction is based on clusters of individual motifs and any combination of these into multi-motifs with selectable minimal and maximal distances. Individual motifs can be of heterogenous classes, such as simple sequence motifs or position-specific scoring matrices. Cluster scores are weighted occurrences of multi-motifs, where the weights are derived from positive and negative training sets. We illustrate the flexibility of the jPREdictor with a new prediction of Polycomb/Trithorax Response Elements in Drosophila melanogaster. jPREdictor is available as a graphical user interface for online use and for download at http://bibiserv.techfak.uni-bielefeld.de/jpredictor.
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Fiedler T, Rehmsmeier M. jPREdictor: a versatile tool for the prediction of cis-regulatory elements. Nucleic Acids Research. 2006;34(Web Server):W546-W550.
Fiedler, T., & Rehmsmeier, M. (2006). jPREdictor: a versatile tool for the prediction of cis-regulatory elements. Nucleic Acids Research, 34(Web Server), W546-W550.
Fiedler, T., and Rehmsmeier, M. (2006). jPREdictor: a versatile tool for the prediction of cis-regulatory elements. Nucleic Acids Research 34, W546-W550.
Fiedler, T., & Rehmsmeier, M., 2006. jPREdictor: a versatile tool for the prediction of cis-regulatory elements. Nucleic Acids Research, 34(Web Server), p W546-W550.
T. Fiedler and M. Rehmsmeier, “jPREdictor: a versatile tool for the prediction of cis-regulatory elements”, Nucleic Acids Research, vol. 34, 2006, pp. W546-W550.
Fiedler, T., Rehmsmeier, M.: jPREdictor: a versatile tool for the prediction of cis-regulatory elements. Nucleic Acids Research. 34, W546-W550 (2006).
Fiedler, Thomas, and Rehmsmeier, Marc. “jPREdictor: a versatile tool for the prediction of cis-regulatory elements”. Nucleic Acids Research 34.Web Server (2006): W546-W550.
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10 References

Data provided by Europe PubMed Central.

Genome-wide prediction of Polycomb/Trithorax response elements in Drosophila melanogaster.
Ringrose L, Rehmsmeier M, Dura JM, Paro R., Dev. Cell 5(5), 2003
PMID: 14602076
Transcriptional control in the segmentation gene network of Drosophila.
Schroeder MD, Pearce M, Fak J, Fan H, Unnerstall U, Emberly E, Rajewsky N, Siggia ED, Gaul U., PLoS Biol. 2(9), 2004
PMID: 15340490
A new approach to text searching
Baeza-Yates R.A., Gonnet G.H.., 1992
Recruitment of Drosophila Polycomb group proteins to chromatin by DSP1.
Dejardin J, Rappailles A, Cuvier O, Grimaud C, Decoville M, Locker D, Cavalli G., Nature 434(7032), 2005
PMID: 15791260
A conserved sequence motif in Polycomb-response elements.
Mihaly J, Mishra RK, Karch F., Mol. Cell 1(7), 1998
PMID: 9651590
The DNA-binding polycomb group protein pleiohomeotic mediates silencing of a Drosophila homeotic gene.
Fritsch C, Brown JL, Kassis JA, Muller J., Development 126(17), 1999
PMID: 10433918

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