ProkFunFind

ProkFunFind integrates multiple search approaches and annotation types to annotate microbial functions and identify gene clusters of interest.

Key Features:

• Hierarchical Function Definitions: Biological functions are defined hierarchically, allowing individual genes to be identified using heterogeneous search terms.
• Multiple Search Term Types: Supports sequences, profile hidden Markov models, protein domains, and orthology groups as search terms.
• Flexible and Customizable Searches: Searches can be tailored to specific biological functions.
• Multiple Output Formats: Search results are output in multiple formats to facilitate downstream analyses.
• Gene Cluster Identification: Identifies gene clusters encoding complex biological functions composed of multiple genes.

Scientific Applications:

• Bacterial Flagella Identification: Demonstrated utility in searching for gene clusters encoding flagellar genes, which are complex organelles composed of multiple genes.
• Microbial Genome Annotation: Facilitates meaningful analysis of new and existing microbial genomes by integrating multiple types of annotation and sequence data.
• Metabolic Function Prediction: Supports prediction of metabolic functions in microbial genomes.
• Virulence Factor Identification: Supports identification of virulence factors in microbial genomes.
• Microbial Evolution Studies: Supports understanding the evolution of microbes through integrated genome analysis.

Methodology:

ProkFunFind incorporates multiple search approaches and annotation types, using hierarchical definitions of biological functions where individual genes are identified through heterogeneous search terms consisting of sequences, profile hidden Markov models, protein domains, and orthology groups.