Abstract
RPFdb (http://www.rpfdb.org or http://sysbio.sysu.edu.cn/rpfdb) is a public database for hosting, analyzing and visualizing ribosome profiling (ribo-seq) data. Since its initial release in 2015, the amount of new ribo-seq data has been considerably enlarged with the increasing popularity of ribo-seq technique. Here, we describe an updated version, RPFdb v2.0, which brings significant data expansion, feature improvements, and functionality optimization: (i) RPFdb v2.0 currently hosts 2884 ribo-seq datasets from 293 studies, covering 29 different species, in comparison with 777 datasets from 82 studies and 8 species in the previous version; (ii) A refined analysis pipeline with multi-step quality controls has been applied to improve the pre-processing and alignment of ribo-seq data; (iii) New functional modules have been added to provide actively translated open reading frames (ORFs) information for each ribo-seq data; (iv) More features have been made available to increase database usability. With these additions and enhancements, RPFdb v2.0 will represent a more valuable and comprehensive database for the gene regulation community.
Highlights
Ribosome profiling is emerging as a powerful technique that enables genome-wide investigation of in vivo translation at sub-codon resolution [1,2]
Several databases are designed for storing genomic elements detected from ribo-seq, such as sORFs.org [11] and uORFdb [12], hosting small open reading frames (ORFs) and upstream ORFs respectively
In line with the significant expansion of ribo-seq data available in the database, we have made several major improvements in this release, including a refined analysis pipeline with multi-step quality control applied for improving the pre-processing and alignment of ribo-seq data, new functional modules providing actively translated ORFs information, and more web features for better database usability
Summary
Ribosome profiling is emerging as a powerful technique that enables genome-wide investigation of in vivo translation at sub-codon resolution [1,2]. Since the initial release of RPFdb in 2015, the volume of raw riboseq data in repositories such as the Sequence Read Archive (SRA) [13] has grown rapidly because of the increasing popularity of ribo-seq technique and reduction of sequencing costs. The rapidly accumulating ribo-seq data provide a basis for discovering the ‘dark matter’ in the genome and understanding the components of the translation apparatus.
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