Inparanoid

Inparanoid identifies and clusters orthologous proteins between genomes to support comparative and evolutionary genomics across 17 complete genomes including Anopheles gambiae, Caenorhabditis briggsae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Takifugu rubripes, Gallus gallus, Homo sapiens, Mus musculus, Pan troglodytes, Rattus norvegicus, Oryza sativa, Plasmodium falciparum, Arabidopsis thaliana, Escherichia coli, Saccharomyces cerevisiae, and Schizosaccharomyces pombe.

Key Features:

• Ortholog identification: Produces pairwise ortholog groups between genomes based on sequence similarity.
• Dataset composition: Covers 17 complete genomes spanning metazoans, plants, fungi, a protist, and a bacterium (Escherichia coli).
• Proteome sourcing: Uses complete proteomes extracted from Ensembl and UniProt.
• Pairwise BLAST comparisons: Performs pairwise sequence comparisons using BLAST (Basic Local Alignment Search Tool) to detect potential orthologs.
• Reciprocal best-hit seeding: Initiates clusters with reciprocally best-matching ortholog pairs that serve as seeds.
• Inparalog clustering: Groups inparalogs—genes within the same species that diverged after a speciation event—around seed pairs.
• Outparalog exclusion: Systematically excludes outparalogs, i.e., genes that diverged by duplication prior to speciation, from ortholog clusters.

Scientific Applications:

• Evolutionary biology: Enables analysis of gene conservation and divergence across the included species.
• Functional genomics: Supports transfer of functional annotations via orthology to predict functions of uncharacterized genes.
• Comparative genomics: Facilitates comparative analyses of gene repertoires across multiple genomes.
• Phylogenetic analysis: Provides ortholog groups useful for reconstructing evolutionary histories and phylogenetic inference.

Methodology:

Complete proteomes are extracted from Ensembl and UniProt; pairwise sequence comparisons are performed using BLAST; the Inparanoid algorithm clusters potential orthologs by initiating clusters with reciprocally best-matching ortholog seeds, grouping inparalogs around those seeds, and excluding outparalogs.