FoldAtlas: A repository for genome-wide RNA structure probing data

Matthew Norris, Chun Kit Kwok, Jitender Cheema, Matthew Hartley, Richard J. Morris, Sharon Aviran, Yiliang Ding

Research output: Contribution to journalArticle

7 Scopus citations

Abstract

Summary: Most RNA molecules form internal base pairs, leading to a folded secondary structure. Some of these structures have been demonstrated to be functionally significant. High-throughput RNA structure chemical probing methods generate millions of sequencing reads to provide structural constraints for RNA secondary structure prediction. At present, processed data from these experiments are difficult to access without computational expertise. Here we present FoldAtlas, a web interface for accessing raw and processed structural data across thousands of transcripts. FoldAtlas allows a researcher to easily locate, view, and retrieve probing data for a given RNA molecule. We also provide in silico and in vivo secondary structure predictions for comparison, visualized in the browser as circle plots and topology diagrams. Data currently integrated into FoldAtlas are from a new high-depth Structure-seq data analysis in Arabidopsis thaliana, released with this work.

Original languageEnglish (US)
Pages (from-to)306-308
Number of pages3
JournalBioinformatics
Volume33
Issue number2
DOIs
StatePublished - Jan 15 2017

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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    Norris, M., Kwok, C. K., Cheema, J., Hartley, M., Morris, R. J., Aviran, S., & Ding, Y. (2017). FoldAtlas: A repository for genome-wide RNA structure probing data. Bioinformatics, 33(2), 306-308. https://doi.org/10.1093/bioinformatics/btw611