ElemeNT – a computational tool for detecting core promoter elements

Core promoter elements play a pivotal role in the transcriptional output, yet they are often detected manually within sequences of interest. Here, researchers from Bar-Ilan University present 2 contributions to the detection and curation of core promoter elements within given sequences:

1. First, the Elements Navigation Tool (ElemeNT) is a user-friendly web-based, interactive tool for prediction and display of putative core promoter elements and their biologically-relevant combinations.
2. Second, the CORE database summarizes ElemeNT-predicted core promoter elements near CAGE and RNA-seq-defined Drosophila melanogaster transcription start sites (TSSs).

ElemeNT’s predictions are based on biologically-functional core promoter elements, and can be used to infer core promoter compositions. ElemeNT does not assume prior knowledge of the actual TSS position, and can therefore assist in annotation of any given sequence. These resources facilitate the identification of core promoter elements as active contributors to gene expression.

In the output table, the elements are ordered by their type and then sorted by PWM scores . The MTE, DPE and Bridge motifs, which are strictly dependent on the presence of a functional initiator, are displayed immediately below the corresponding initiator. For TATA box motifs, a message is displayed if the specific TATA box is located 26 to 40 bp upstream of the A+1 of an initiator. In addition, a message is displayed if a BRE^u or BRE^d is located in close proximity to the specific TATA box.

Availability – http://lifefaculty.biu.ac.il/gershon-tamar/index.php/resources