Orthologue Search Service

Orthologue Search Service performs orthologue detection and phylogenetic reconciliation by integrating BLAST (Basic Local Alignment Search Tool) homolog retrieval, multiple sequence alignment, gene and species tree construction, bootstrapped tree analysis, and reconciliation to distinguish orthologues from paralogues.

Key Features:

• BLAST Integration: Retrieves homologous protein sequences using BLAST (Basic Local Alignment Search Tool) from sequence databases.
• Gene and Species Tree Construction: Constructs gene trees for selected sequences and corresponding species (phylogenetic) trees for the involved taxa.
• Reconciliation Methodology: Employs a reconciliation method that assumes gene duplications when gene and species trees mismatch to predict orthologues and paralogues.
• Multiple Alignment Construction: Builds multiple sequence alignments for selected BLAST hits either globally or for specific local regions.
• Bootstrapped Tree Analysis: Generates bootstrapped phylogenetic trees to assess support and compares them to the species tree to identify discrepancies.

Scientific Applications:

• Functional annotation: Identifies orthologues to support functional assignment and prediction of protein functions across species and in newly sequenced genomes.
• Evolutionary and phylogenetic analysis: Improves accuracy of phylogenetic studies and evolutionary models by distinguishing orthologues from paralogues and revealing gene duplication and speciation events.
• Comparative genomics: Facilitates comparative analyses across species by providing reconciled gene and species tree relationships.

Methodology:

Input protein sequence → BLAST retrieval of homologs → selection of sequences → multiple sequence alignment (global or local) → construction of gene trees and species trees → reconciliation assuming gene duplications to resolve mismatches → generation and comparison of bootstrapped trees to the species tree.