GWIPS-viz: development of a ribo-seq genome browser

AM Michel, G Fox, A M. Kiran, C De Bo… - Nucleic acids …, 2014 - academic.oup.com
AM Michel, G Fox, A M. Kiran, C De Bo, PBF O'Connor, SM Heaphy, JPA Mullan
Nucleic acids research, 2014academic.oup.com
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 …
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.
Oxford University Press