rVista

rVista identifies evolutionarily conserved transcription factor binding site (TFBS) patterns in noncoding DNA to characterize regulatory modules across species.

Key Features:

• Integration of multiple analytical approaches: Combines TFBS predictions, sequence comparisons, and cluster analysis to detect conserved regulatory modules in noncoding DNA.
• Evolutionary conservation prioritization: Uses evolutionary conservation to prioritize candidate regulatory elements conserved across related species.
• Compatibility with alignment programs (version 2.0): Processes alignments generated by zPicture and blastz and accepts pre-computed pairwise alignments from vertebrate genomes available through the ECR Browser and the GALA database.
• Integration with TRANSFAC: Interconnects with the TRANSFAC database to access positional weight matrices, enabling searches of existing matrices and definition of custom consensus sequences.

Scientific Applications:

• Identification of functional noncoding elements: Detects conserved TFBS patterns to prioritize candidate regulatory sequences for experimental validation.
• Comparative regulatory genomics: Enables cross-species analysis of conserved regulatory modules using pairwise alignments and TFBS conservation.
• Analysis of transcriptional regulation: Maps TFBS clusters and conserved motifs to investigate transcriptional dynamics and regulatory architecture.
• Evolutionary and biomedical studies: Supports studies of regulatory evolution and gene expression mechanisms relevant to development and disease.

Methodology:

Combines TFBS prediction, sequence comparisons, and cluster analysis; processes zPicture and blastz alignments and pre-computed pairwise alignments (ECR Browser, GALA); queries TRANSFAC matrices and permits custom consensus sequences.