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Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
Semi-automated update and cleanup of structural RNA alignment databases
J Gorodkin1, C Zwieb, B Knudsen
1Department of Ecology and Genetics, The Institute of Biological Sciences, University of Aarhus, Building 540, Ny Munkegade, DK-8000 Aarhus C, Denmark.
Bioinformatics (Oxford, England)
|July 13, 2001
Summary
New software improves structural RNA database maintenance by automating sequence alignment and consistency checks. This reduces sequence misannotations, enhancing data accuracy for RNA research.
Area of Science:
- Bioinformatics
- Computational Biology
- Molecular Biology
Background:
- Structural RNA databases are crucial for understanding RNA function.
- Maintaining the accuracy and completeness of these databases is challenging.
- Existing methods may lead to sequence misannotations.
Purpose of the Study:
- To develop and present a suite of computational tools for the automated maintenance of structural RNA databases.
- To enhance the accuracy of RNA sequence annotations and structural alignments.
Main Methods:
- A primary program performs BLAST searches against GenBank to extend and realign RNA sequences.
- Subsequent programs analyze base pair consistency and phylogenetic support for database entries.
- Iterative refinement of structural alignments is facilitated by the program outputs.
Main Results:
- The developed programs automate critical steps in database maintenance, including sequence extension and realignment.
- The tools enable rigorous examination of base pair consistency and phylogenetic support.
- Application to the Signal Recognition Particle RNA database reduced potential misannotations per sequence from 20 to 3.
Conclusions:
- The developed software suite effectively automates and refines the maintenance of structural RNA databases.
- These tools significantly improve the accuracy of RNA sequence data, reducing misannotations.
- The methods provide a robust framework for iterative refinement of structural RNA database alignments.
