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

Show simple item record

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.date.accessioned 2017-11-14T13:24:30Z
dc.date.available 2017-11-14T13:24:30Z
dc.date.issued 2014
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.volume 42
dc.identifier.issued D1
dc.identifier.startpage 859
dc.identifier.endpage 864
dc.identifier.issn 0305-1048
dc.identifier.issn 1362-4962
dc.identifier.uri http://hdl.handle.net/10468/5018
dc.identifier.doi 10.1093/nar/gkt1035
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.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher Oxford University Press en
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
dc.internal.authorcontactother Pavel V. Baranov, Biochemistry & Cell Biology, University College Cork, Cork, Ireland. +353-21-490-3000 Email: P.Baranov@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.contributor.funder Wellcome Trust
dc.contributor.funder Science Foundation Ireland
dc.description.status Peer reviewed en
dc.identifier.journaltitle Nucleic Acids Research en
dc.internal.IRISemailaddress p.baranov@ucc.ie 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)./


Files in this item

This item appears in the following Collection(s)

Show simple item record

© 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. Except where otherwise noted, this item's license is described as © 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.
This website uses cookies. By using this website, you consent to the use of cookies in accordance with the UCC Privacy and Cookies Statement. For more information about cookies and how you can disable them, visit our Privacy and Cookies statement