GWIPS-viz: 2018 update

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dc.contributor.author Michel, Audrey M.
dc.contributor.author Kiniry, Stephen J.
dc.contributor.author O'Connor, Patrick B. F.
dc.contributor.author Mullan, James P.
dc.contributor.author Baranov, Pavel V.
dc.date.accessioned 2017-10-06T15:40:39Z
dc.date.available 2017-10-06T15:40:39Z
dc.date.issued 2017-09-05
dc.identifier.citation Michel, A. M., Kiniry, S. J., O’Connor, Patrick B. F., Mullan, J. P. and Baranov, P. V. (2017) 'GWIPS-viz: 2018 update', Nucleic Acids Research, gkx790 (8pp). doi:10.1093/nar/gkx790 en
dc.identifier.startpage gkx790-1 en
dc.identifier.endpage gkx790-8 en
dc.identifier.issn 0305-1048
dc.identifier.uri http://hdl.handle.net/10468/4844
dc.identifier.doi 10.1093/nar/gkx790
dc.description.abstract The GWIPS-viz browser (http://gwips.ucc.ie/) is an on-line genome browser which is tailored for exploring ribosome profiling (Ribo-seq) data. Since its publication in 2014, GWIPS-viz provides Ribo-seq data for an additional 14 genomes bringing the current total to 23. The integration of new Ribo-seq data has been automated thereby increasing the number of available tracks to 1792, a 10-fold increase in the last three years. The increase is particularly substantial for data derived from human sources. Following user requests, we added the functionality to download these tracks in bigWig format. We also incorporated new types of data (e.g. TCP-seq) as well as auxiliary tracks from other sources that help with the interpretation of Ribo-seq data. Improvements in the visualization of the data have been carried out particularly for bacterial genomes where the Ribo-seq data are now shown in a strand specific manner. For higher eukaryotic datasets, we provide characteristics of individual datasets using the RUST program which includes the triplet periodicity, sequencing biases and relative inferred A-site dwell times. This information can be used for assessing the quality of Ribo-seq datasets. To improve the power of the signal, we aggregate Ribo-seq data from several studies into Global aggregate tracks for each genome. en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher Oxford University Press (OUP) en
dc.rights © The Authors 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com en
dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/ en
dc.subject Genome en
dc.subject Bacterial en
dc.subject Periodicity en
dc.subject Ribosome en
dc.subject RNA en
dc.subject Messenger en
dc.subject Triplets en
dc.subject Datasets en
dc.title GWIPS-viz: 2018 update en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Pavel Baranov, School Of 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.date.updated 2017-10-06T15:25:10Z
dc.description.version Published Version en
dc.internal.rssid 413831583
dc.contributor.funder Science Foundation Ireland en
dc.contributor.funder Irish Research Council en
dc.description.status Peer reviewed en
dc.identifier.journaltitle Nucleic acids research en
dc.internal.copyrightchecked No !!CORA!! en
dc.internal.licenseacceptance Yes 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)./ en


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© The Authors 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Except where otherwise noted, this item's license is described as © The Authors 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
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