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.
Highlights
Ribosome profiling is based on the isolation of messenger RNA fragments protected by ribosomes followed by massively parallel sequencing of the protected fragments or footprints
We describe the development of genome-wide information on protein synthesis (GWIPS)-viz, an online genome browser for viewing ribosome profiling data
Ribosome profiling 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 fragments, which allows the ribosome density along all mRNA transcripts present in the cell to be quantified
Summary
Ribosome profiling is based on the isolation of messenger RNA (mRNA) fragments protected by ribosomes followed by massively parallel sequencing of the protected fragments or footprints. The time required to download, preprocess and align the raw data may be the most limiting factor of all for timepoor researchers To address these issues, we introduce GWIPS-viz (http://gwips.ucc.ie), a free online browser that is prepopulated with published ribo-seq data. In GWIPS-viz, users can search for their gene(s) of interest in the genome(s) for which ribo-seq data are available and view a snapshot of the gene’s translation under the conditions of the experiment. The latter gene apparently uses two sites of translation initiation for its expression
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