RPFdb V2.0: an Updated Database for Genome-wide Information of Translated MRNA Generated from Ribosome Profiling

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2018 Oct 19

PMID 30335166

Citations 31

Authors

Hongwei Wang

Ludong Yang

Yan Wang

Leshi Chen

Huihui Li

Zhi Xie

Affiliations

Soon will be listed here.

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.

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