Consite

Consite identifies conserved transcription factor binding sites and cis-regulatory elements in genomic sequences by combining phylogenetic footprinting with metazoan transcription factor binding models to improve prediction of functional regulatory regions.

Key Features:

• Phylogenetic footprinting: Employs cross-species comparison to detect conserved regulatory sequences, exploiting selective pressure to distinguish functional regions and increasing predictive selectivity compared to single-sequence analysis, reportedly by an order of magnitude.
• High-quality transcription factor models: Integrates binding-site predictions from a comprehensive collection of experimentally-confirmed metazoan transcription factor binding profiles to refine site identification.
• Orthologous sequence analysis: Retrieves and analyzes orthologous regulatory sequences to identify conserved elements across species for comparative studies.
• Conserved TF-binding site identification and alignment: Identifies conserved transcription-factor-binding sites, including paired alignments of sites in orthologous sequences, to support promoter architecture analyses.

Scientific Applications:

• Gene regulation studies: Infers regulatory mechanisms by locating conserved transcription factor binding sites linked to gene expression control.
• Comparative genomics: Detects evolutionary conservation of regulatory elements across species using orthologous sequence comparisons.
• Promoter analysis: Enhances signal-to-noise for detailed examination of promoter regions and transcriptional control elements.

Methodology:

Performs phylogenetic footprinting via cross-species sequence comparison to identify conserved regions under selective pressure and integrates experimentally-confirmed metazoan transcription factor binding profiles to refine binding-site predictions.