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.
