title: ElemeNT: a computational tool for detecting core promoter elements.
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.
authors.affiliation: a The Mina and Everard Goodman Faculty of Life Sciences ; Bar-Ilan University ; Ramat Gan , Israel.
authors.forename: Anna
authors.initials: A
authors.lastname: Sloutskin
authors.forename: Yehuda M
authors.initials: YM
authors.lastname: Danino
authors.forename: Yaron
authors.initials: Y
authors.lastname: Orenstein
authors.forename: Yonathan
authors.initials: Y
authors.lastname: Zehavi
authors.forename: Tirza
authors.initials: T
authors.lastname: Doniger
authors.forename: Ron
authors.initials: R
authors.lastname: Shamir
authors.forename: Tamar
authors.initials: T
authors.lastname: Juven-Gershon
mesh_terms: D000818:Animals; D019295:Computational Biology; D062126:Databases, Chemical; D004331:Drosophila melanogaster; D011401:Promoter Regions, Genetic; D012984:Software; D024363:Transcription Initiation Site
keywords: BRE; BRE downstream of the TATA box; BREu; BRE upstream of the TATA box; DCE; DPE; MTE; RNA Polymerase II; TBP; RNAP II transcription; TATA box; TATA box-binding protein; TAFs; TBP-associated factors; TSS; TCT; TFIIB recognition element; BREd; computational tool; core promoter elements/motifs; downstream core element; DPE; downstream core promoter element; Inr; initiator; initiator; MTE; motif 10 element; PWM; position weight matrix; RNAP II; promoter prediction; transcription start site.