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A collection of computationally predicted R-loop forming sequences (RLFSs). R-loopDB is a comprehensive database of RLFSs in eight organisms, i.e. human, chimp, mouse, rat, chicken, frog, fruit fly and yeast, that offers benefits for the researchers who study R-loop related human diseases using these species. The combination of several other data resources, such as RLFS strand, GC skew value and experimental R-loop detection data, could provide more information for advanced analyses and predictions. R-loopDB allows searching of RLFSs in the genes and in the 2 kb upstream and downstream flanking sequences of any gene. R-loopDB exploits the Ensembl gene annotation system, providing users with chromosome coordinates, sequences, gene and genomic data of the 1,565,795 RLFSs distributed in 121,056 genic or proximal gene regions of the covered organisms.

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R-loopDB specifications

Restrictions to use:
None
Community driven:
No
User data submission:
Not allowed
Database management system:
MySQL
Data access:
Web user interface
Version:
2

Publications

  • (Jenjaroenpun et al., 2016) R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops. Nucleic Acids Research.
    PMID: 27899586

R-loopDB support

Documentation

Credits

Institution(s)

Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore; Systems Biology and Bioinformatics Research, Pilot Plant Development and Training Institute, King Mongkut's University of Technology, Thonburi, Bangkok, Thailand; School of Computer Engineering, Nanyang Technological University, Singapore

Funding source(s)

This work was supported by the Biomedical Research Council of the Agency for Science, Technology and Research (A*STAR), Singapore.

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