Computational resources for ribosome profiling: from database to Web server and software

Wang, Hongwei; Wang, Yan

doi:10.1093/bib/bbx093

Cited by 43 publications

(42 citation statements)

References 68 publications

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“…While these usually offer more flexibility than online tools, they do require the user to download and install the software along with its dependencies. The currently available software resources for exploring Ribo-seq data have been reviewed in detail in Calviello & Ohler (2017) and Wang, Wang, & Xie, 2017).…”

Section: Figure 11mentioning

confidence: 99%

The GWIPS‐viz Browser

Kiniry

Michel

Baranov

2018

CP in Bioinformatics

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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. © 2018 by John Wiley & Sons, Inc.

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Section: Figure 11mentioning

confidence: 99%

The GWIPS‐viz Browser

Kiniry

Michel

Baranov

2018

CP in Bioinformatics

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“…While a range of computational approaches have been developed for ribosome profiling, they either focus solely on ~28 nt footprints (Berg et al, 2019;Popa et al, 2016), or directly rely on alignment files for analyses and do not consider RPF length as a major design feature (Carja et al, 2017;Chung et al, 2015;Perkins et al, 2019;Birkeland et al, 2018). Moreover, existing software often lags behind high-quality standards in installation, ease of use, documentation, and portability (Wang et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

RiboFlow, RiboR and RiboPy: An ecosystem for analyzing ribosome profiling data at read length resolution

Özadam

Geng

Cenik

2019

Preprint

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Ribosome occupancy measurements enable protein abundance estimation and infer mechanisms of translation. Recent studies have revealed that sequence read lengths in ribosome profiling data are highly variable and carry critical information. Consequently, data analyses require the computation and storage of multiple metrics for a wide range of ribosome footprint lengths. We developed a software ecosystem including a new efficient binary file format named 'ribo'. Ribo files store all essential data grouped by ribosome footprint lengths. Users can assemble ribo files using our RiboFlow pipeline that processes raw ribosomal profiling sequencing data. RiboFlow is highly portable and customizable across a large number of computational environments with built-in capabilities for parallelization. We also developed interfaces for writing and reading ribo files in the R (RiboR) and Python (RiboPy) environments. Using RiboR and RiboPy, users can efficiently access ribosome profiling quality control metrics, generate essential plots, and carry out analyses. Altogether, these components create a complete software ecosystem for researchers to study translation through ribosome profiling. Availability and ImplementationFor a quickstart, please see https://ribosomeprofiling.github.io. Source code, installation instructions and links to documentation are available on GitHub: https://github.com/ribosomeprofiling

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“…Many tools have also been developed to process users’ own ribo-seq data (16). For example, using RiboGalaxy (17), users without bioinformatics expertise can check the quality of their ribo-seq data, align their ribo-seq data to the genome or the transcriptome and visualize the results.…”

Section: Introductionmentioning

confidence: 99%

“…A description of other tools [e.g. SORFs.org (20), MTDR (21), SPECtre (22), TISdb (23), RiboDiff (24) and PUNCH-P (25)] can be seen in the review paper (16). …”

Section: Introductionmentioning

confidence: 99%

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HRPDviewer: human ribosome profiling data viewer

Jiang

Chang

et al. 2018

Database

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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 address these two challenges, we developed the Human Ribosome Profiling Data viewer (HRPDviewer). HRPDviewer (i) contains 610 published human ribo-seq datasets from Gene Expression Omnibus, (ii) aligns the ribo-seq data to the transcriptome and (iii) provides visualization of the ribo-seq data on the selected mRNA transcripts. Using HRPDviewer, researchers can compare the ribosome binding patterns of multiple mRNA transcripts from the same gene or different genes to gain an accurate understanding of protein synthesis in human cells. We believe that HRPDviewer is a useful resource for researchers to study translational regulation in human.Database URL: http://cosbi4.ee.ncku.edu.tw/HRPDviewer/ or http://cosbi5.ee.ncku.edu.tw/HRPDviewer/

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Computational resources for ribosome profiling: from database to Web server and software

Cited by 43 publications

References 68 publications

The GWIPS‐viz Browser

The GWIPS‐viz Browser

RiboFlow, RiboR and RiboPy: An ecosystem for analyzing ribosome profiling data at read length resolution

HRPDviewer: human ribosome profiling data viewer

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