RPFdb specifications


Unique identifier OMICS_10197
Name RPFdb
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 2.0
Maintained Yes


  • Bacteria
    • Escherichia coli
  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Arabidopsis thaliana
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
  • Vertebrates
    • Danio rerio


  • person_outline Zhi Xie

Publications for RPFdb

RPFdb citations


riboviz: analysis and visualization of ribosome profiling datasets

BMC Bioinformatics
PMCID: 5657068
PMID: 29070028
DOI: 10.1186/s12859-017-1873-8

[…] all analyses and visualization. Lack of open source code also limits the use of these tools for analyzing ribosome-profiling datasets in non-model organisms. In addition, tools such as RiboGalaxy and RPFdb are limited by computational resources available on the host servers and can lead to long lag times.To address these limitations, we have developed an open-source bioinformatics toolkit, riboviz […]


Insights into the mechanisms of eukaryotic translation gained with ribosome profiling

Nucleic Acids Res
PMCID: 5314775
PMID: 27923997
DOI: 10.1093/nar/gkw1190

[…] lyse their data on a cloud server via an internet browser using a variety of tools from such packages as RUST (), riboSeqR () and RiboTools (). Publicly available RiboSeq data also can be accessed at RPFdb (). Furthermore, sORFs.org () collects ORFs whose translation is supported with RiboSeq data, and TISdb () is a collection of translation initiation sites predicted from RiboSeq data. Several st […]

RPFdb institution(s)
State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China; Centre for Advanced Computational Solutions (C-fACS), Lincoln University, New Zealand
RPFdb funding source(s)
Supported by National Natural Science Foundation of China [31871302, 31829002].

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