DCODE.ORG

DCODE.ORG provides a suite of comparative genomics analysis tools for identifying conserved genomic elements, cis-regulatory modules, transcription factor binding sites, and lineage-specific functional regions across vertebrate and invertebrate genomes.

Key Features:

• zPicture: Visualizes pairwise sequence alignments and highlights conserved regions across genomes.
• Mulan: Performs multiple sequence alignments of arbitrary sequences to identify conserved elements across species.
• eShadow: Applies phylogenetic shadowing to detect lineage- and species-specific functional elements in non-coding genomic regions.
• rVista: Identifies conserved transcription factor binding sites by combining sequence conservation with transcription factor motif analysis.
• multiTF: Analyzes conserved transcription factor binding sites across multiple transcription factors and species.
• CREME 2.0: Extracts cis-regulatory modules (CRMs) that coordinate expression of co-regulated genes.
• ECR Browser: Provides access to multiple vertebrate and invertebrate genome alignments to inspect evolutionary conserved regions.

Scientific Applications:

• Functional region demarcation: Demarcates conserved and functional regions within anonymous DNA sequences using comparative alignments.
• Lineage-specific element discovery: Identifies lineage- and species-specific functional elements via phylogenetic shadowing and conservation analysis.
• Transcription factor binding site analysis: Detects conserved transcription factor binding sites across species to infer regulatory function.
• Cis-regulatory module discovery: Extracts and characterizes cis-regulatory modules involved in coordinated gene expression.
• Comparative genomics and evolutionary conservation studies: Supports comparative analysis of vertebrate and invertebrate genomes to study evolutionary conservation.
• Novel gene identification and regulatory mechanism elucidation: Aids identification of novel genes and dissection of gene regulatory mechanisms through conserved element and CRM analysis.

Methodology:

Comparative sequence analysis, phylogenetic shadowing, and evolutionary conservation analysis are used to compare genomic sequences across species, identify conserved elements and lineage-specific functional regions, and analyze transcription factor binding sites.