TREND Protein Evolution Function

TREND Protein Evolution Function performs tree-based integration and automated analysis of homologous proteins, protein domain architectures, and gene neighborhoods to infer protein function and study protein evolution.

Key Features:

• Automated Integration: Automates preparation and integration of data relating homologous proteins, domain architectures, and gene neighborhoods to phylogenetic contexts.
• Phylogenomic Contextualization: Places derived information into a phylogenomic framework to explore evolutionary relationships among proteins across species.
• Adjustable Components: Provides configurable computational components to tailor analyses to specific datasets and research questions.
• Data Integration with Databases: Integrates data from RefSeq, Pfam, CDD, and MiST for enriched annotation of protein features and gene neighborhoods.
• Clustering of Neighboring Genes: Clusters neighboring genes to characterize operons and genomic organization relevant to protein function evolution.

Scientific Applications:

• Protein function inference: Infers protein function by combining homology, domain architecture, and gene neighborhood evidence in an evolutionary context.
• Evolutionary relationship analysis: Investigates evolutionary histories of protein families within a phylogenomic framework.
• Gene neighborhood and operon studies: Examines gene neighborhood organization and operon structure to assess their impact on protein function and evolution.

Methodology:

Tree-based exploration of neighborhoods and domains with automated integration of homologous proteins and domain architectures, clustering of neighboring genes, and placement of derived information into a phylogenomic context.