GWIPS-viz: Development of a Ribo-Seq Genome Browser

Nucleic Acids Res. 2014 Jan;42(Database issue):D859-64. doi: 10.1093/nar/gkt1035. Epub 2013 Oct 31.

Abstract

We describe the development of GWIPS-viz (http://gwips.ucc.ie), an online genome browser for viewing ribosome profiling data. Ribosome profiling (ribo-seq) is a recently developed technique that provides genome-wide information on protein synthesis (GWIPS) in vivo. It is based on the deep sequencing of ribosome-protected messenger RNA (mRNA) fragments, which allows the ribosome density along all mRNA transcripts present in the cell to be quantified. Since its inception, ribo-seq has been carried out in a number of eukaryotic and prokaryotic organisms. Owing to the increasing interest in ribo-seq, there is a pertinent demand for a dedicated ribo-seq genome browser. GWIPS-viz is based on The University of California Santa Cruz (UCSC) Genome Browser. Ribo-seq tracks, coupled with mRNA-seq tracks, are currently available for several genomes: human, mouse, zebrafish, nematode, yeast, bacteria (Escherichia coli K12, Bacillus subtilis), human cytomegalovirus and bacteriophage lambda. Our objective is to continue incorporating published ribo-seq data sets so that the wider community can readily view ribosome profiling information from multiple studies without the need to carry out computational processing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Databases, Genetic*
  • Genome*
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Internet
  • Mice
  • Protein Biosynthesis*
  • RNA, Messenger / chemistry
  • Ribosomes / metabolism
  • Sequence Alignment
  • Sequence Analysis, RNA*
  • Web Browser*

Substances

  • RNA, Messenger