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The ITS2 Database
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Updates to the RNA mapping database (RMDB), version 2.

Joseph D Yesselman1, Siqi Tian1, Xin Liu2

  • 1Department of Biochemistry, Stanford University School of Medicine, Stanford CA 94305, USA.

Nucleic Acids Research
|July 28, 2018
PubMed
Summary
This summary is machine-generated.

The RNA Mapping Database (RMDB) now centralizes over 800 RNA chemical mapping datasets, offering interactive visualization of RNA structure and function. This resource aids researchers in understanding RNA biology through comprehensive chemical mapping data.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Bioinformatics

Background:

  • Chemical mapping is essential for studying RNA structure and function.
  • The volume of RNA chemical mapping data is rapidly increasing.
  • A centralized repository is needed to manage this growing dataset.

Purpose of the Study:

  • To establish and maintain a comprehensive database for RNA chemical mapping data.
  • To provide an updated and user-friendly interface for accessing and visualizing RNA mapping information.
  • To facilitate the deposition of new chemical mapping data.

Main Methods:

  • Creation and curation of the RNA Mapping Database (RMDB).
  • Integration of data from various chemical mapping techniques, including multidimensional methods.
  • Redesign of the database interface with interactive graphical browsing and visualization tools.

Main Results:

  • The RMDB now contains over 800 entries, covering 134,000 RNAs and over 15 million probed residues.
  • The redesigned interface offers interactive visualization of structural, thermodynamic, and kinetic data at single-nucleotide resolution.
  • New deposition tools streamline the process for adding new data to the RMDB.

Conclusions:

  • The RMDB serves as a vital, centralized resource for RNA chemical mapping data.
  • The enhanced interface improves accessibility and utility for researchers studying RNA.
  • The database supports the advancement of RNA biology research by consolidating and presenting complex data.