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Related Experiment Video

Updated: Jul 2, 2025

From a Natural Product to Its Biosynthetic Gene Cluster: A Demonstration Using Polyketomycin from Streptomyces diastatochromogenes Tü6028

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Annotating microbial functions with ProkFunFind.

Keith Dufault-Thompson¹, Xiaofang Jiang¹

¹National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.

|February 16, 2024

Summary

This summary is machine-generated.

ProkFunFind is a new tool that integrates various annotation methods for microbial genome analysis. It offers a flexible approach to identify genes and functions, aiding in understanding microbial evolution and roles.

Keywords:

functional annotation genome annotation genomics

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Last Updated: Jul 2, 2025

From a Natural Product to Its Biosynthetic Gene Cluster: A Demonstration Using Polyketomycin from Streptomyces diastatochromogenes Tü6028

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Published on: January 13, 2017

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Published on: September 15, 2015

Area of Science:

Microbiology
Bioinformatics
Genomics

Background:

Microbial genome analysis is crucial for understanding microbial functions and evolution.
Numerous tools exist for gene identification and annotation, but integrating their results is challenging.
Existing methods for integrating annotation data are often ad hoc, hindering reproducible research.

Purpose of the Study:

To develop ProkFunFind, a flexible and customizable tool to bridge the gap between diverse microbial genome annotation approaches.
To provide a unified platform for annotating microbial functions using heterogeneous search terms.
To facilitate downstream analysis by outputting search results in multiple formats.

Main Methods:

ProkFunFind utilizes hierarchical definitions of biological functions.
It supports heterogeneous search terms including sequences, profile hidden Markov models, protein domains, and orthology groups.
The tool was demonstrated by searching for bacterial flagellar gene clusters.

Main Results:

ProkFunFind successfully integrated multiple annotation types and search strategies.
The tool demonstrated flexibility in tailoring searches to specific biological functions.
Application in identifying bacterial flagella showcased its utility in complex gene cluster searches.

Conclusions:

ProkFunFind offers an accessible and flexible solution for annotating biological functions in microbial genomes.
It enables reproducible integration of diverse annotation and sequence data.
The tool facilitates meaningful analysis of microbial genomes by identifying gene clusters of interest.