OrthoVenn

OrthoVenn compares orthologous gene clusters across multiple species to enable genome-wide comparative genomics analyses of protein function and evolution.

Key Features:

• Extensive Species Coverage: Supports comparisons among vertebrates, metazoa, protists, fungi, plants, and bacteria.
• Custom Sequence Uploads: Accepts user-uploaded protein sequences from user-defined species for inclusion in analyses.
• Venn Diagram Visualization: Generates Venn diagrams that represent overlaps among orthologous clusters and provides summary counts and functional summaries.
• In-depth Cluster Analysis: Performs detailed sequence-based analyses and annotations of orthologous clusters using sequence analysis tools.
• Single-Copy Gene Identification: Identifies orthologous clusters composed of single-copy genes useful for evolutionary and phylogenetic studies.
• Customized Search Capabilities: Enables keyword and BLAST (Basic Local Alignment Search Tool) searches to locate specific gene clusters.

Scientific Applications:

• Evolutionary Relationship Inference: Elucidates evolutionary relationships by identifying shared and lineage-specific orthologous clusters.
• Functional Conservation and Pathway Inference: Infers conserved biological processes and pathways from overlapping orthologous clusters and functional summaries.
• Protein Function Inference: Facilitates transfer and annotation of protein function across species through orthologous cluster comparison.
• Phylogenetic Analyses: Supports phylogenetic and lineage-tracing studies using identified single-copy orthologs.

Methodology:

Comparison and annotation of orthologous gene clusters using sequence analysis tools; BLAST searches for cluster retrieval; computation of cluster overlaps represented as Venn diagrams with summary counts and functional summaries; identification of single-copy orthologous clusters; in-depth sequence analyses of clusters.