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Compilation of small ribosomal subunit RNA structures

J M Neefs1, Y Van de Peer, P De Rijk

  • 1Departement Biochemie, Universiteit Antwerpen (UIA), Belgium.

Nucleic Acids Research
|July 1, 1993
PubMed
Summary

A comprehensive database of small ribosomal subunit RNA structures was compiled, containing 1804 sequences. This resource aids comparative studies and phylogenetic tree reconstruction for molecular biology research.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Small ribosomal subunit RNA (srRNA) is crucial for protein synthesis.
  • Understanding srRNA structure is key to deciphering its function and evolutionary relationships.
  • A centralized, curated database is needed for efficient analysis of srRNA sequences.

Purpose of the Study:

  • To create and maintain a comprehensive database of small ribosomal subunit RNA nucleotide sequences.
  • To facilitate comparative analysis of srRNA higher-order structures.
  • To support the reconstruction of phylogenetic trees using srRNA sequence data.

Main Methods:

  • Compilation of 1804 srRNA nucleotide sequences from diverse sources (eukaryotic, archaeal, bacterial, plastidial, mitochondrial).

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  • Storage of sequences in an alignment format for comparative studies.
  • Inclusion of secondary structure elements indicated by special symbols.

    • Main Results:

    • The database contains 1804 srRNA nucleotide sequences as of April 23, 1993.
    • Sequence distribution includes 365 eukaryotic, 65 archaeal, 1260 bacterial, 30 plastidial, and 84 mitochondrial sequences.
    • The aligned format and secondary structure annotations enhance usability for research.

    Conclusions:

    • The compiled srRNA database provides a valuable resource for molecular biology research.
    • The database facilitates comparative structural analysis and phylogenetic studies.
    • Accessibility via online (FTP, email) and CD-ROM ensures broad scientific community access.