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The Analysis of Regulatory DNA: Current Developments, Knowledge and Applications Uncovering Gene Regulation
Editor(s): Kenneth Berendzen
Co-Editor(s): Joachim Kilian and Dierk Wanke
eISBN: 978-1-60805-492-3   ISBN: 978-1-60805-711-5   
Chapter PDF Price: $15
   



Identifying Cis Elements In Eukaryotes Using Old Tricks And High Throughput Sequence Data

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Author(s): Björn Usadel, Kenneth W. Berendzen and Anthony Bolger
Chapter DOI: 10.2174/9781608054923113010011
Page: 162-175 (14)

Abstract:
Bioinformatics and especially sequence analysis has come a long way. Nevertheless, finding cis elements is still difficult, as one is usually confronted with several problems simultaneously, hindering the efficient identification of cis elements. Here, we describe the general structure of a core promoter including its known elements and then move on to finding regulatory cis regulatory elements that might drive the expression of a gene. We review several commonly used tools and briefly touch on the techniques these use and conclude by showing that next generation sequencing techniques might provide enough additional information to make reliable cis element identification easier in the future.
Keywords:
cis elements, core promoter, TATA box, cis element detection, position weight matricies, IUPAC, k-mers, probablistic methods, cis element prediction, 1001 genome project, Arabidopsis, plants, cis element detection, in silico.
Affiliation:
RWTH Aachen University, Biology I, Worringerweg 1, 50262 Aachen, Germany & Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich, Leo-Brandt-Straße, 52425 Jülich, Germany.