HRPDviewer: human ribosome profiling data viewer

Database : the Journal of Biological Databases and Curation
Wei-Sheng WuJoseph T Tseng

Abstract

Translational regulation plays an important role in protein synthesis. Dysregulation of translation causes abnormal cell physiology and leads to diseases such as inflammatory disorders and cancers. An emerging technique, called ribosome profiling (ribo-seq), was developed to capture a snapshot of translation. It is based on deep sequencing of ribosome-protected mRNA fragments. A lot of ribo-seq data have been generated in various studies, so databases are needed for depositing and visualizing the published ribo-seq data. Nowadays, GWIPS-viz, RPFdb and TranslatomeDB are the three largest databases developed for this purpose. However, two challenges remain to be addressed. First, GWIPS-viz and RPFdb databases align the published ribo-seq data to the genome. Since ribo-seq data aim to reveal the actively translated mRNA transcripts, there are advantages of aligning ribo-req data to the transcriptome over the genome. Second, TranslatomeDB does not provide any visualization and the other two databases only provide visualization of the ribo-seq data around a specific genomic location, while simultaneous visualization of the ribo-seq data on multiple mRNA transcripts produced from the same gene or different genes is desired. To addres...Continue Reading

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Citations

Nov 25, 2019·Wiley Interdisciplinary Reviews. RNA·Stephen J KiniryPavel V Baranov
May 5, 2021·Database : the Journal of Biological Databases and Curation·Tzu-Hsien YangCheng-Tse Liu
May 6, 2021·Nucleic Acids Research·Stephen J KiniryPavel V Baranov

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