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, we present 2 contributions to the detection and curation of core promoter elements within given sequences. First, the Elements Navigation Tool (ElemeNT)...

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Bibliographic Details
Published in:Transcription 2015-05, Vol.6 (3), p.41-50
Main Authors: Sloutskin, Anna, Danino, Yehuda M, Orenstein, Yaron, Zehavi, Yonathan, Doniger, Tirza, Shamir, Ron, Juven-Gershon, Tamar
Format: Article
Language:English
Subjects:
Animals
BRE
Computational Biology
computational tool
core promoter elements/motifs
Databases, Chemical
DPE
Drosophila melanogaster
initiator
MTE
promoter prediction
Promoter Regions, Genetic
RNAP II transcription
Short
Software
TATA box
TCT
Transcription Initiation Site
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Summary: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.
ISSN:2154-1264
2154-1272
DOI:10.1080/21541264.2015.1067286