ElemeNT 2023

ElemeNT 2023 predicts and curates core promoter elements and transcription factor binding sites to analyze transcription initiation and the quality of high-throughput transcription start site (TSS) datasets.

Key Features:

• Detection and Curation: Detects and curates core promoter elements within nucleotide sequences and identifies user-defined motifs, including sequence-specific DNA binding sites.
• Evolutionary Conservation Assessment: Assesses evolutionary conservation of promoter elements across species.
• High-Throughput TSS Dataset Evaluation: Evaluates the quality of high-throughput transcription start site (TSS) datasets using preferential motif positioning.
• Expanded CORE Database: Maintains an expanded CORE database with predicted core promoter elements around annotated TSSs for ten species ranging from worms to humans.

Scientific Applications:

• Transcription Initiation Studies: Identifies core promoter elements and transcription factor binding sites to elucidate mechanisms of transcription initiation at specific loci.
• Evolutionary Insights: Compares promoter element conservation across species to inform evolutionary dynamics of promoter architecture.
• TSS Quality Appraisal: Appraises the quality of high-throughput TSS datasets through analysis of motif positioning and prevalence.
• Synthetic Promoter Design: Provides detailed information on core promoter composition and motif prevalence to support synthetic promoter design.

Methodology:

Integrates capabilities for assessing evolutionary conservation and evaluating TSS dataset quality, leverages preferential motif positioning to improve prediction accuracy, and uses an expanded CORE database of predicted core promoter elements around annotated TSSs for ten species (worms to humans).