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SeQuery: an interactive graph database for visualizing the GPCR superfamily.

Geng-Ming Hu1, M K Secario1,2, Chi-Ming Chen1

  • 1Department of Physics, National Taiwan Normal University, 88 Sec. 4 Ting-Chou Rd., Taipei 11677, Taiwan.

Database : the Journal of Biological Databases and Curation
|June 26, 2019
PubMed
Summary
This summary is machine-generated.

SeQuery is a new tool that visualizes protein and gene networks. It accurately identifies G protein-coupled receptors (GPCRs) and explores their superfamily relationships.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics and Proteomics

Background:

  • The rapid discovery of novel protein and gene sequences in the omics era presents challenges for biological characterization.
  • Efficient analysis of complex biological networks requires integrated data and intuitive visualization tools.

Purpose of the Study:

  • To develop SeQuery, a web-based graphical database tool for visualizing proteome/genome networks.
  • To enable efficient identification and characterization of protein sequences within biological superfamilies.
  • To provide a comprehensive, interactive exploration of biological networks, exemplified by the G protein-coupled receptor (GPCR) superfamily.

Main Methods:

  • Development of a web-based graphical database tool (SeQuery).
  • Integration of sequential, structural, and functional information from databases like UniProt, GPCRdb, and RCSB PDB.
  • Construction of a graph database for the G protein-coupled receptor (GPCR) superfamily.
  • Testing SeQuery's accuracy using the GPCR2841 dataset.

Main Results:

  • SeQuery successfully identifies 99 out of 100 queried protein sequences in the GPCR superfamily.
  • The tool provides intuitive visualization of proteome/genome networks.
  • Demonstrated ability to define sequential and functional roles within the GPCR superfamily.

Conclusions:

  • SeQuery offers an effective solution for analyzing and visualizing complex biological sequence data.
  • The tool facilitates a comprehensive understanding of biological superfamilies through interactive graph exploration.
  • SeQuery is adaptable for other biological networks and can be expanded with additional databases.