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PANNOTATOR: an automated tool for annotation of pan-genomes
A R Santos1, E Barbosa, K Fiaux
1Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil.
Genetics and Molecular Research : GMR
|September 26, 2013
Summary
PANNOTATOR is a new web-based pipeline for bacterial pan-genome annotation. It automates the process, ensuring high accuracy for gene names and functions, surpassing existing tools for bacterial research.
Area of Science:
- Genomics
- Bioinformatics
- Microbial research
Background:
- Next-generation sequencing accelerates bacterial genome deposition.
- Pan-genomic studies require high-quality genome assembly and functional annotation.
- Investigating strain phenotypic differences necessitates accurate genotypic analysis.
Purpose of the Study:
- To develop an automated pipeline for bacterial pan-genome annotation.
- To ensure quality and standardization in functional genome annotation across strains.
- To reduce manual effort in generating genome annotation reports and corrections.
Main Methods:
- Developed PANNOTATOR, a web-based automated annotation pipeline.
- Utilized annotation transfer with a 70% similarity cut-off.
- Compared PANNOTATOR's performance against a gold standard and other software (RAST, BASys).
Main Results:
- PANNOTATOR achieved 98% correctness for gene names and 76% for functions.
- Outperformed RAST and BASys by significant margins in gene name and function annotation.
- Demonstrated fast and reliable pan-genome annotation capabilities.
Conclusions:
- PANNOTATOR provides efficient and accurate bacterial pan-genome annotation.
- Facilitates research focus on key genotypic differences between bacterial strains.
- Establishes a new standard for automated functional genome annotation in pan-genomic studies.
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