ConTrav2

ConTrav2 identifies and visualizes transcription factor binding sites (TFBS) across specified genomic regions to support analysis of gene regulatory elements.

Key Features:

• Cross-Species Analysis: Supports analysis across nine reference organisms, including human and yeast, enabling comparative assessment of TFBS conservation and divergence.
• Genomic Region Coverage: Analyzes promoters, 5'-UTRs, 3'-UTRs, introns, and other regions surrounding coding or non-coding genes.
• Position Weight Matrix Library: Provides access to hundreds of position weight matrices (PWMs) and accepts user-uploaded custom matrices for TFBS prediction.
• Gene and Transcript Selection: Permits specification of target genes and transcripts to focus TFBS analysis on precise genomic contexts.
• TFBS Visualization: Visualizes predicted TFBS within the selected genomic regions.

Scientific Applications:

• Gene Regulation: Identification of potential TFBS to infer regulatory mechanisms governing gene expression.
• Comparative Genomics: Comparative analysis of TFBS across multiple species to study evolutionary conservation of transcriptional regulation.
• Disease Research: Analysis of TFBS associated with disease-related genes to investigate molecular mechanisms of conditions.

Methodology:

Selection of the genomic region surrounding a gene or transcript, specification of gene and transcript, and prediction of TFBS using a library of PWMs or user-uploaded matrices.