HHCompare

HHCompare compares Hidden Markov Models (HMMs) using HMM–HMM comparisons and hierarchical clustering to identify and analyze potential paralogues and gene duplication events that contribute to protein diversification.

Key Features:

• HMM-HMM Comparison: Employs HMM-HMM comparisons to detect similarities between sequence models and sequences for identification of duplicated genes.
• Hierarchical Clustering: Uses hierarchical clustering to group related HMMs and sequences and to organize relationships among gene families.
• Detection of Gene Duplications: Identifies potential paralogues and gene duplication events that may underlie functional and protein diversification.
• Phylogenetic Validation: Methodology was validated using standard phylogeny methods.

Scientific Applications:

• Toxin Diversification Studies: Applied to the coral Acropora digitifera genome, HHCompare identified 55 potential toxin-encoding genes, of which 36 (65%) were likely derived from gene duplication events.
• Evolutionary Biology: Enables examination of how gene duplication contributes to phenotypic diversity and adaptation across gene families.

Methodology:

Integrates HMM-HMM comparison techniques with hierarchical clustering algorithms, with results validated using standard phylogeny methods.