ElemeNT: a computational tool for detecting core promoter elements

Anna Sloutskin, Yehuda M. Danino, Yaron Orenstein, Yonathan Zehavi, Tirza Doniger, Ron Shamir, Tamar Juven-Gershon

Research output: Contribution to journalArticlepeer-review

31 Scopus citations

Abstract

Core promoter elements play a pivotal role in the transcriptional output, yet they are often detected manually within sequences of interest. Here, we present 2 contributions to the detection and curation of core promoter elements within given sequences. 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. 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, freely accessible at http://lifefaculty.biu.ac.il/gershon-tamar/index.php/resources, facilitate the identification of core promoter elements as active contributors to gene expression.

Original languageEnglish
Pages (from-to)41-50
Number of pages10
JournalTranscription
Volume6
Issue number3
DOIs
StatePublished - 27 May 2015
Externally publishedYes

Keywords

  • BRE
  • DPE
  • MTE
  • RNAP II transcription
  • TATA box
  • TCT
  • computational tool
  • core promoter elements/motifs
  • initiator
  • promoter prediction

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