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The GWIPS-viz browser
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Accepted Version
Date
2018-05-16
Authors
Kiniry, Stephen J.
Michel, Audrey M.
Baranov, Pavel V.
Journal Title
Journal ISSN
Volume Title
Publisher
John Wiley & Sons, Inc.
Published Version
Abstract
GWIPS-viz is a publicly available browser that provides Genome Wide Information on Protein Synthesis through the visualization of ribosome profiling data. Ribosome profiling (Ribo-seq) is a high-throughput technique which isolates fragments of messenger RNA that are protected by the ribosome. The alignment of the ribosome-protected fragments or footprint sequences to the corresponding reference genome and their visualization using GWIPS-viz allows for unique insights into the genome loci that are expressed as potentially translated RNA. The GWIPS-viz browser hosts both Ribo-seq data and corresponding mRNA-seq data from publicly available studies across a number of genomes, avoiding the need for computational processing on the user side. Since its initial publication in 2014, over 1885 tracks have been produced across 24 genomes. This unit describes the navigation of the GWIPS-viz genome browser, the uploading of custom tracks, and the downloading of the Ribo-seq/mRNA-seq alignment data.
Description
Keywords
Genome browser , Gene expression , Protein synthesis , Ribosome profiling , Translation , GWIPS-viz , mRNA-seq
Citation
Kiniry, S. J., Michel, A. M. and Baranov, P. V. (2018) 'The GWIPS-viz browser', Current Protocols in Bioinformatics, 62(1), e50. doi:10.1002/cpbi.50
Copyright
© 2018, John Wiley & Sons Inc. This is the accepted manuscript version of the following article: Kiniry, S. J., Michel, A. M. and Baranov, P. V. (2018) 'The GWIPS-viz browser', Current Protocols in Bioinformatics, 62(1), e50. doi:10.1002/cpbi.50, which has been published in final form at https://doi.org/10.1002/cpbi.50. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.