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NGPINT V3: a containerized orchestration Python software for discovery of next-generation protein-protein

Schuyler D Smith1,2, Valeria Velásquez-Zapata1,2, Roger P Wise1,3

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NGPINT V3 offers a containerized solution for yeast two-hybrid (Y2H) next-generation sequencing data analysis. This update resolves installation issues, improving protein-protein interaction screening accessibility.

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Genomics

Background:

  • Yeast two-hybrid (Y2H) assays coupled with next-generation sequencing (NGS) are powerful tools for studying protein-protein interactions.
  • The NGPINT software facilitates the analysis of large datasets generated by Y2H-NGS screens.
  • Previous versions of NGPINT faced compatibility and dependency challenges, hindering widespread adoption and effective use.

Purpose of the Study:

  • To address the installation and operational issues of the NGPINT software.
  • To provide an updated, accessible, and robust version of NGPINT for Y2H-NGS data analysis.
  • To ensure continued compatibility with companion software like Y2H-SCORES.

Main Methods:

  • Containerization of NGPINT using Singularity and Docker technologies.
  • Streamlining software dependencies for easier installation and execution.
  • Hosting container images on platforms like Sylabs and Dockerhub for broad accessibility.

Main Results:

  • NGPINT V3 is now compatible with diverse operating systems and computing environments.
  • The containerized implementation simplifies the integration of NGPINT into high-throughput and cloud-computing workflows.
  • Easier adoption and utilization of NGPINT for analyzing complex protein-protein interaction data.

Conclusions:

  • NGPINT V3 represents a significant advancement in analyzing Y2H-NGS data, overcoming previous limitations.
  • The containerized approach enhances the accessibility and usability of sophisticated bioinformatics tools.
  • This update supports more effective and efficient research into protein-protein interactions.