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GWIPS-viz: development of a ribo-seq genome browser
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.
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.
Keyword(s): Generation sequencing data; High-resolution view; In-vivo; Nucleotide resolution; Profiling reveals; Translation; Elongation; Alignment; Database; Extensions
Publication Date:
2014
Type: Journal article
Peer-Reviewed: Yes
Language(s): English
Institution: University College Cork
Funder(s): Science Foundation Ireland
Citation(s): 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
Publisher(s): Oxford University Press
File Format(s): application/pdf
Related Link(s): https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkt1035
First Indexed: 2017-11-15 06:30:10 Last Updated: 2017-11-21 06:30:47