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.