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PGAP-X: extension on pan-genome analysis pipeline.
Yongbing Zhao1,2, Chen Sun1,2, Dongyu Zhao1,2
1CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
BMC Genomics
|January 25, 2018
Summary
PGAP-X is a new software tool that helps researchers visualize and interpret bacterial genomics data. It analyzes genome alignment, gene clustering, and genetic variations, revealing insights into bacterial evolution and diversity.
Area of Science:
- Bacterial genomics
- Computational biology
- Bioinformatics
Background:
- The pan-genome analysis pipeline (PGAP) is widely used in bacterial genomics.
- Interpreting and visualizing PGAP results remains a challenge for researchers.
Purpose of the Study:
- To develop a novel, cross-platform software named PGAP-X.
- To enhance the interpretation and visualization of bacterial genomic data.
Main Methods:
- PGAP-X integrates modules for whole genome alignment, orthologous gene clustering, pan-genome profile analysis, and genetic variant analysis.
- Includes visualization tools for genome structure comparison, gene distribution, pan-genome profiles, and genetic variations.
- Supports importing data from other similar software for further analysis.
Main Results:
- PGAP-X was tested on *Streptococcus pneumoniae* and *Chlamydia trachomatis* strains.
- *S. pneumoniae* strains exhibit greater genomic and gene content diversity compared to *C. trachomatis*.
- Analysis suggests *S. pneumoniae* has undergone significant evolutionary events like rearrangements and horizontal gene transfer.
Conclusions:
- PGAP-X provides intuitive visualization of bacterial genomic diversity.
- Facilitates understanding of bacterial genome dynamics and evolution.
- Source code and executables are freely available.
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