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NGPINT: a next-generation protein-protein interaction software.

Sagnik Banerjee1,2, Valeria Velásquez-Zapata1,3, Gregory Fuerst3,4

  • 1Program in Bioinformatics & Computational Biology, Iowa State University, Ames, IA, 50011, USA.

Briefings in Bioinformatics
|December 28, 2020
PubMed
Summary
This summary is machine-generated.

NGPINT is a new software tool that efficiently identifies protein-protein interactions using high-throughput yeast-two hybrid (Y2H) assays. It accurately detects interactions from sequencing data, aiding in understanding cellular signaling networks.

Keywords:
3-frame cDNA libraryautomated softwarenext-generation interaction screeningprotein–protein interactionyeast-two hybrid

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Area of Science:

  • Proteomics
  • Systems Biology
  • Bioinformatics

Background:

  • Mapping protein-protein interactions (PPIs) is crucial for understanding cellular signaling.
  • High-throughput yeast-two hybrid (Y2H) assays coupled with next-generation sequencing offer a scalable solution for PPI discovery.
  • Analyzing large-scale Y2H data presents computational challenges.

Purpose of the Study:

  • To develop a robust and scalable software tool, NGPINT, for identifying protein interactors from high-throughput Y2H data.
  • To facilitate the analysis of PPIs in batch culture across various organisms.

Main Methods:

  • NGPINT integrates sequence read alignment, prey fragment reconstruction, and gene enrichment analysis.
  • It identifies in-frame translational fusion reads between Y2H transcription factors and cDNA fragments to minimize false positives.
  • The software processes data from any biosystem with available genome or transcriptome references.

Main Results:

  • NGPINT achieved 95% accuracy in simulated interaction detection.
  • The software successfully identified all validated interactions in published datasets.
  • It demonstrated robustness and scalability for analyzing Y2H data.

Conclusions:

  • NGPINT provides an efficient and accurate computational solution for large-scale PPI mapping using Y2H assays.
  • This tool can accelerate the discovery of PPIs in both model and non-model organisms.
  • NGPINT enhances the utility of high-throughput Y2H for systems biology research.