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MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes.

Carlos A Ruiz-Perez¹, Roth E Conrad², Konstantinos T Konstantinidis^3,4,5,6

¹School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.

BMC Bioinformatics

|January 7, 2021

Summary

This summary is machine-generated.

MicrobeAnnotator is a new, automated pipeline for microbial genome functional annotation. It integrates multiple databases, provides metabolic summaries, and is efficient for personal computers.

Keywords:

Comparative genomics Genome annotation Metabolic potential Protein annotation

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Area of Science:

Microbiology
Bioinformatics
Genomics

Background:

High-throughput sequencing generates numerous microbial genomes.
Existing genome annotation tools lack integration and user-friendliness.
There is a need for efficient, comprehensive microbial genome analysis pipelines.

Purpose of the Study:

To develop an automated, user-friendly pipeline for comprehensive microbial genome functional annotation.
To integrate results from multiple reference protein databases.
To provide summarized metabolic reconstructions and facilitate genome comparison.

Main Methods:

Developed MicrobeAnnotator, a Python 3-based automated pipeline.
Integrated multiple protein databases: KEGG Orthology (KO), Enzyme Commission (E.C.), Gene Ontology (GO), Pfam, and InterPro.
Implemented graphical output (heatmap) for metabolic module comparison.

Main Results:

MicrobeAnnotator provides comprehensive functional annotations with linked metadata.
The pipeline generates summarized KEGG modules for easy comparison of multiple genomes.
Annotated 100 Escherichia coli and 78 Candidate Phyla Radiation (CPR) bacterial genomes.

Conclusions:

MicrobeAnnotator recovers more annotations per genome compared to faster, reduced-database tools.
The pipeline is computationally efficient and suitable for personal computers.
Its output is easily integrated into other analysis pipelines.