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Related Experiment Videos

tmRDB (tmRNA database).

B Knudsen1, J Wower, C Zwieb

  • 1Department of Genetics and Ecology, The Institute of Biological Sciences, University of Aarhus, Building 540, Ny Munkegade, DK-8000 Aarhus C, Denmark.

Nucleic Acids Research
|January 11, 2000
PubMed
Summary
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The tmRNA database (tmRDB) now includes 86 tmRNAs, offering insights into this essential molecule for bacterial trans-translation. This update enhances data accessibility and computational usability for researchers studying tmRNA functions.

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • tmRNA, a unique molecule combining transfer RNA (tRNA) and messenger RNA (mRNA) functions, plays a crucial role in bacterial trans-translation.
  • This molecule is widespread, found in most bacteria and in organelles like chloroplasts and mitochondria.
  • Understanding tmRNA is vital for deciphering gene expression regulation and protein synthesis in prokaryotes and some eukaryotes.

Purpose of the Study:

  • To update and expand the tmRNA database (tmRDB) with new sequences and associated data.
  • To provide researchers with comprehensive and accessible information on tmRNA.
  • To improve the usability of tmRNA data for computational analysis.

Main Methods:

  • Curated collection and integration of new tmRNA sequences.

Related Experiment Videos

  • Bioinformatic analysis for predicting tmRNA-encoded tag peptides.
  • Generation of tmRNA alignments using manual curation and computational tools.
  • Development of secondary structures and 3D models in PDB format.

    • Main Results:

    • The tmRDB now contains 86 tmRNAs, an increase of 26 sequences from the previous release.
    • Predicted tmRNA-encoded tag peptides are provided for each sequence.
    • tmRNA alignments with structural annotations are available in multiple formats, including a new, computationally friendly column format.
    • Secondary structures and 3D models are accessible for representative tmRNAs.

    Conclusions:

    • The updated tmRDB serves as a valuable resource for studying tmRNA and trans-translation.
    • Enhanced data formats and structural information facilitate further research and computational analysis.
    • The database expansion supports a deeper understanding of tmRNA's role across diverse organisms.