School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
Nucleic Acids Res. 2018 Jan 4;46(D1):D823-D830. doi: 10.1093/nar/gkx790.
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.
GWIPS-viz 浏览器（http://gwips.ucc.ie/）是一个在线基因组浏览器，专门用于探索核糖体分析（Ribo-seq）数据。自 2014 年发布以来，GWIPS-viz 为另外 14 个基因组提供了 Ribo-seq 数据，目前总数达到 23 个。新的 Ribo-seq 数据的整合已经实现自动化，从而将可用轨道的数量增加到 1792 个，这是过去三年来增加的 10 倍。对于源自人类来源的数据，这种增加尤其显著。根据用户的要求，我们添加了以 bigWig 格式下载这些轨道的功能。我们还整合了新类型的数据（例如 TCP-seq）以及来自其他来源的辅助轨道，这些数据有助于解释 Ribo-seq 数据。数据可视化方面的改进尤其针对细菌基因组，现在以特定链的方式显示 Ribo-seq 数据。对于高等真核数据集，我们使用 RUST 程序提供各个数据集的特征，包括三联体周期性、测序偏差和相对推断的 A 位停留时间。这些信息可用于评估 Ribo-seq 数据集的质量。为了提高信号的强度，我们将来自多个研究的 Ribo-seq 数据汇总到每个基因组的 Global aggregate 轨道中。
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