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

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dc.contributor.authorMichel, Audrey M.
dc.contributor.authorFox, Gearoid
dc.contributor.authorKiran, Anmol M.
dc.contributor.authorDe Bo, Christof
dc.contributor.authorO'Connor, Patrick B. F.
dc.contributor.authorHeaphy, Stephen M.
dc.contributor.authorMullan, James P. A.
dc.contributor.authorDonohue, Claire A.
dc.contributor.authorHiggins, Desmond G.
dc.contributor.authorBaranov, Pavel V.
dc.contributor.funderWellcome Trust
dc.contributor.funderScience Foundation Ireland
dc.date.accessioned2017-11-14T13:24:30Z
dc.date.available2017-11-14T13:24:30Z
dc.date.issued2014
dc.description.abstractWe 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.sponsorshipScience Foundation Ireland (12/IA/1335); Wellcome Trust (094423)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationMichel, 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/gkt1035en
dc.identifier.doi10.1093/nar/gkt1035
dc.identifier.endpage864
dc.identifier.issn0305-1048
dc.identifier.issn1362-4962
dc.identifier.issuedD1
dc.identifier.journaltitleNucleic Acids Researchen
dc.identifier.startpage859
dc.identifier.urihttps://hdl.handle.net/10468/5018
dc.identifier.volume42
dc.language.isoenen
dc.publisherOxford University Pressen
dc.relation.projectinfo: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.urihttps://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.urihttps://creativecommons.org/licenses/by/3.0/
dc.subjectGeneration sequencing dataen
dc.subjectHigh-resolution viewen
dc.subjectIn-vivoen
dc.subjectNucleotide resolutionen
dc.subjectProfiling revealsen
dc.subjectTranslationen
dc.subjectElongationen
dc.subjectAlignmenten
dc.subjectDatabaseen
dc.subjectExtensionsen
dc.titleGWIPS-viz: development of a ribo-seq genome browseren
dc.typeArticle (peer-reviewed)en
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