HogProf

HogProf performs large-scale phylogenetic profiling using hierarchical orthologous groups (HOGs) and minhash-based locality-sensitive hashing to identify protein families with shared evolutionary histories and predict gene functional associations.

Key Features:

• Scalability: Handles the vast number of genes present in eukaryotic genomes and avoids quadratic time or worse scaling relative to gene count.
• Efficiency: Utilizes minhash-based data structures and locality-sensitive hashing to enable rapid construction and querying of large phylogenetic profiles.
• Orthology-Based Profiling: Leverages orthologous group information and hierarchical orthologous groups (HOGs) to group genes and detect protein families that are jointly retained or lost across lineages.
• Broad Applicability: Applies to organisms across bacteria, archaea, and eukaryotes for large-scale phylogenetic studies.

Scientific Applications:

• Comparative Performance: Has demonstrated superior performance compared to traditional phylogeny-based methods such as the Enhanced Phylogenetic Tree.
• Network Reconstruction: Reconstructs biological networks and identifies interactors of complex protein assemblies, exemplified by analyses of the kinetochore complex.
• Conserved Reproduction Proteins: Queries and identifies conserved proteins involved in sexual reproduction, including Hap2, Spo11, and Gex1.

Methodology:

Constructs phylogenetic profiles using hierarchical orthologous groups (HOGs) and employs minhash-based data structures with locality-sensitive hashing for efficient retrieval of similar profiles.