PHROG

PHROG clusters prokaryotic viral proteins into remote homologous groups using HMM profile-profile comparisons to improve functional annotation and comparative analysis of viral protein families.

Key Features:

• Remote Homology Detection: Uses HMM profile-profile comparisons to detect distant homologous relationships among viral proteins.
• Large-scale Clustering: Processes 17,473 reference prokaryotic viruses and their proteins, clustering 868,340 of 938,864 proteins into 38,880 groups.
• Depth and Homogeneity: Produces clustering depth reported as twice that of classical methods while maintaining homogeneity within clusters.
• Cluster Annotation Coverage: Includes manual inspection against reference sequence databases to annotate 5,108 clusters, covering 50.6% of the protein dataset and classified into nine viral-specific functional categories.

Scientific Applications:

• Functional Annotation: Provides annotated clusters for viral proteins, covering 5,108 clusters (50.6% of proteins) assigned to nine functional categories.
• Comparative Analysis: Supplies a detailed classification of viral protein families to support comparative analyses and investigation of evolutionary patterns and ecological roles.
• Annotation of New Sequences: Supports annotation of future prokaryotic viral sequences to aid studies of virus evolution and ecology.

Methodology:

Clusters are generated using HMM profile-profile comparisons for remote homology detection and grouping of proteins into homogeneous clusters based on distant evolutionary relationships.