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RiboD: a comprehensive database for prokaryotic riboswitches.

Sumit Mukherjee1, Sukhen Das Mandal2, Nikita Gupta3

  • 1Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.

Bioinformatics (Oxford, England)
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Summary

We developed RiboD, a database for prokaryotic riboswitches. This resource aids in understanding riboswitch-mediated gene regulation in bacteria and archaea by providing detailed location and regulatory information.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Riboswitches are non-coding RNA elements that regulate gene expression.
  • They control gene expression through conformational changes triggered by ligand binding.
  • Understanding riboswitch function is crucial for deciphering gene regulation in prokaryotes.

Purpose of the Study:

  • To create a comprehensive database of prokaryotic riboswitches.
  • To facilitate the search and extraction of information on riboswitch location and regulated genes.
  • To provide a valuable resource for studying riboswitch-based gene regulation.

Main Methods:

  • Development of a curated database for prokaryotic riboswitches.
  • Implementation of multi-criteria search functionalities.
  • Data extraction for riboswitch location and associated genes/operons.

Main Results:

  • A comprehensive database, RiboD, cataloging prokaryotic riboswitches has been established.
  • Users can efficiently search and retrieve specific riboswitch information.
  • Detailed data on riboswitch genomic locations and their regulated genes/operons are available.

Conclusions:

  • RiboD serves as a significant resource for researchers studying prokaryotic gene regulation.
  • The database enhances the understanding of riboswitch mechanisms in bacteria and archaea.
  • Facilitates further research into riboswitch-mediated gene control.