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Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data.

Tiago F Jesus1, Bruno Ribeiro-Gonçalves1, Diogo N Silva1

  • 1Instituto de Microbiologia and Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisboa, Portugal.

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Summary

Plasmid ATLAS is a web tool for exploring plasmid relationships in NCBI RefSeq. It aids in searching plasmid metadata and visualizing plasmid evolution for better interpretation of sequencing data.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Plasmids are crucial mobile genetic elements in bacteria, influencing evolution and antibiotic resistance.
  • Accessing and analyzing vast plasmid data from public repositories like NCBI RefSeq can be challenging.
  • Understanding plasmid relationships and evolution is key to combating antimicrobial resistance.

Purpose of the Study:

  • To develop an accessible database and visualization tool for exploring NCBI RefSeq plasmids.
  • To facilitate the search and analysis of plasmid metadata and evolutionary relationships.
  • To aid in the interpretation of plasmid identification results from high-throughput sequencing data.

Main Methods:

  • Developed Plasmid ATLAS (pATLAS), a web-accessible database.
  • Integrated visual analytics tools for network exploration of plasmid relationships.
  • Implemented search functionalities for plasmid name, host, genes, families, and sequence properties.
  • Enabled integration of external plasmid identification pipeline results into the network visualization.
  • Provided data export to JSON and a REST-API for programmatic access.

Main Results:

  • pATLAS offers intuitive searching of plasmids and associated metadata from NCBI RefSeq.
  • The visual network graph allows exploration of plasmid evolutionary connections.
  • Users can interpret and refine results from external analysis pipelines by contextualizing them within the pATLAS network.
  • Data sharing and re-evaluation are supported through JSON export.
  • REST-API enables integration with other bioinformatics tools.

Conclusions:

  • Plasmid ATLAS simplifies the exploration of plasmid diversity and relationships within public databases.
  • The tool enhances the interpretation of complex genomic data, particularly for plasmid identification.
  • pATLAS serves as a valuable resource for researchers studying plasmid biology, evolution, and epidemiology.