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GWIPS-viz: 2018 update.

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The GWIPS-viz genome browser now offers ribosome profiling (Ribo-seq) data for 23 genomes, with automated updates and enhanced visualization tools for quality assessment and data interpretation.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • The GWIPS-viz browser, established in 2014, serves as a specialized online platform for exploring ribosome profiling (Ribo-seq) data.
  • The demand for comprehensive Ribo-seq data analysis has grown significantly, necessitating updates and expanded functionalities.

Purpose of the Study:

  • To enhance the GWIPS-viz browser by integrating a larger and more diverse collection of Ribo-seq datasets.
  • To improve data accessibility, visualization, and quality assessment tools for Ribo-seq analysis.
  • To facilitate the interpretation of Ribo-seq data through the inclusion of auxiliary data types and aggregated tracks.

Main Methods:

  • Automated integration of new Ribo-seq data for 14 additional genomes, expanding the total to 23.
  • Implementation of download functionality for tracks in bigWig format.
  • Incorporation of new data types like TCP-seq and auxiliary tracks.
  • Strand-specific visualization for bacterial Ribo-seq data.
  • Application of the RUST program for quality assessment of higher eukaryotic datasets (triplet periodicity, sequencing biases, A-site dwell times).
  • Aggregation of Ribo-seq data into Global aggregate tracks for enhanced signal power.

Main Results:

  • GWIPS-viz now provides Ribo-seq data for 23 genomes, with 1792 tracks available, representing a 10-fold increase in three years.
  • Significant expansion of human Ribo-seq data.
  • New features include bigWig download, TCP-seq data, and auxiliary tracks.
  • Improved visualization, including strand-specific display for bacterial genomes.
  • RUST program provides dataset quality metrics (periodicity, biases, dwell times).
  • Global aggregate tracks enhance signal detection.

Conclusions:

  • The updated GWIPS-viz browser offers a significantly expanded and enhanced resource for Ribo-seq data exploration.
  • New features improve data accessibility, quality assessment, and interpretation, particularly for bacterial and human datasets.
  • GWIPS-viz continues to be a vital tool for researchers studying translation and gene expression at a global scale.