Structator: fast index-based search for RNA sequence-structure patterns
2011
Structator: Fast Search for RNA Sequence-Structure Patterns
publication
Evidence: high
Author Information
Author(s): Meyer Fernando, Kurtz Stefan, Backofen Rolf, Will Sebastian, Beckstette Michael
Primary Institution: Center for Bioinformatics, University of Hamburg
Hypothesis
The new method and software can efficiently match RNA sequence-structure patterns in large databases.
Conclusion
The method's sublinear expected running time makes it suitable for RNA sequence-structure pattern matching in large databases.
Supporting Evidence
- The method runs up to two orders of magnitude faster than previous methods.
- Structator is an open-source software solution for RNA sequence-structure pattern matching.
- The affix array data structure is more space-efficient than traditional suffix trees.
Takeaway
This study introduces a new tool that helps scientists quickly find specific RNA shapes in big databases, making research easier.
Methodology
The method uses affix arrays for efficient bidirectional pattern search in RNA databases.
Limitations
The method may not perform as well for RNA patterns with long unconserved loop regions.
Digital Object Identifier (DOI)
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