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

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Date
2014
Authors
Michel, Audrey M.
Fox, Gearoid
Kiran, Anmol M.
De Bo, Christof
O'Connor, Patrick B. F.
Heaphy, Stephen M.
Mullan, James P. A.
Donohue, Claire A.
Higgins, Desmond G.
Baranov, Pavel V.
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Oxford University Press
Published Version
10.1093/nar/gkt1035
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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.
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Keywords
Generation sequencing data , High-resolution view , In-vivo , Nucleotide resolution , Profiling reveals , Translation , Elongation , Alignment , Database , Extensions
Citation
Michel, A. M., Fox, G., Kiran, A. M., De Bo, C., O’Connor, P. B. F., Heaphy, S. M., Mullan, J. P. A., Donohue, C. A., Higgins, D. G. and Baranov, P. V. (2014) 'GWIPS-viz: development of a ribo-seq genome browser', Nucleic Acids Research, 42(D1), pp. 859-864. doi: 10.1093/nar/gkt1035
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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkt1035
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https://hdl.handle.net/10468/5018
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Biochemistry and Cell Biology - Journal Articles
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© 2013, the Authors. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.