GWIPS-viz: development of a ribo-seq genome browser
dc.contributor.author | Michel, Audrey M. | |
dc.contributor.author | Fox, Gearoid | |
dc.contributor.author | Kiran, Anmol M. | |
dc.contributor.author | De Bo, Christof | |
dc.contributor.author | O'Connor, Patrick B. F. | |
dc.contributor.author | Heaphy, Stephen M. | |
dc.contributor.author | Mullan, James P. A. | |
dc.contributor.author | Donohue, Claire A. | |
dc.contributor.author | Higgins, Desmond G. | |
dc.contributor.author | Baranov, Pavel V. | |
dc.contributor.funder | Wellcome Trust | |
dc.contributor.funder | Science Foundation Ireland | |
dc.date.accessioned | 2017-11-14T13:24:30Z | |
dc.date.available | 2017-11-14T13:24:30Z | |
dc.date.issued | 2014 | |
dc.description.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. | en |
dc.description.sponsorship | Science Foundation Ireland (12/IA/1335); Wellcome Trust (094423) | en |
dc.description.status | Peer reviewed | en |
dc.description.version | Published Version | en |
dc.format.mimetype | application/pdf | en |
dc.identifier.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 | en |
dc.identifier.doi | 10.1093/nar/gkt1035 | |
dc.identifier.endpage | 864 | |
dc.identifier.issn | 0305-1048 | |
dc.identifier.issn | 1362-4962 | |
dc.identifier.issued | D1 | |
dc.identifier.journaltitle | Nucleic Acids Research | en |
dc.identifier.startpage | 859 | |
dc.identifier.uri | https://hdl.handle.net/10468/5018 | |
dc.identifier.volume | 42 | |
dc.language.iso | en | en |
dc.publisher | Oxford University Press | en |
dc.relation.project | info:eu-repo/grantAgreement/SFI/SFI Investigator Programme/12/IA/1335/IE/Development of computational resources for the analysis of Genome Wide Information on Protein Synthesis (GWIPS)./ | |
dc.relation.uri | https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkt1035 | |
dc.rights | © 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. | en |
dc.rights.uri | https://creativecommons.org/licenses/by/3.0/ | |
dc.subject | Generation sequencing data | en |
dc.subject | High-resolution view | en |
dc.subject | In-vivo | en |
dc.subject | Nucleotide resolution | en |
dc.subject | Profiling reveals | en |
dc.subject | Translation | en |
dc.subject | Elongation | en |
dc.subject | Alignment | en |
dc.subject | Database | en |
dc.subject | Extensions | en |
dc.title | GWIPS-viz: development of a ribo-seq genome browser | en |
dc.type | Article (peer-reviewed) | en |
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