EvolClust

EvolClust identifies evolutionarily conserved gene clusters by detecting groups of homologous proteins with conserved gene order across multiple eukaryotic genomes.

Key Features:

• Pairwise genome comparisons: Predicts conserved gene clusters by identifying groups of homologous proteins that are consistently co-located in at least two genomes.
• All-versus-all genome comparisons: Infers multi-species cluster families by comparing genomes across a dataset to find related clusters present in multiple species.
• Conservation significance: Detects clusters that are conserved beyond the level expected for the compared genomes.
• Broad taxonomic application: Applied to eukaryotic genomes across five major clades: Fungi, Plants, Metazoans, Insects, and Protists.
• EvolClustDB: Provides pre-computed evolutionarily conserved gene neighborhoods and links gene order information to phylogenetic context to support inference of evolutionary events.

Scientific Applications:

• Evolutionary genomics: Identification of conserved gene clusters to infer potential regulatory or functional associations among genes.
• Inference of evolutionary events: Mapping conserved gene order within phylogenetic contexts to infer gene gain, loss, or transfer.
• Comparative eukaryotic genomics: Discovery and analysis of conserved gene clusters across Fungi, Plants, Metazoans, Insects, and Protists.

Methodology:

Uses pairwise genome comparisons to detect groups of homologous proteins co-located in at least two genomes, employs all-versus-all genome comparisons to infer families of related clusters across species, and pre-computes conserved gene neighborhoods in EvolClustDB for phylogenetic mapping of gene order to infer gain, loss, or transfer.