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Related Experiment Video

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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SICOR: Subgraph Isomorphism Comparison of RNA Secondary Structures.

Michael Schmidt, Kay Hamacher, Felix Reinhardt

    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    |July 12, 2019
    PubMed
    Summary
    This summary is machine-generated.

    We developed SICOR, a new method for comparing RNA secondary structures. SICOR uses graph theory to identify structural similarities, improving RNA aptamer selection in SELEX experiments.

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    Area of Science:

    • Biochemistry
    • Bioinformatics
    • Molecular Biology

    Background:

    • RNA aptamer selection via SELEX relies on RNA secondary structural diversity.
    • Advanced computational methods are needed to effectively analyze and compare these structures.
    • Current comparison methods may not fully capture the nuances of structural similarity.

    Purpose of the Study:

    • To introduce SICOR, a novel computational tool for comparing RNA secondary structures.
    • To evaluate SICOR's performance against existing RNA structure comparison methods.
    • To demonstrate SICOR's utility in enhancing RNA aptamer selection during SELEX.

    Main Methods:

    • Developed SICOR, a method employing probabilistic subgraph isomorphism for RNA secondary structure graph comparison.
    • Utilized graph distance metrics to quantify structural dissimilarities.
    • Benchmarked SICOR against established RNA structure comparison algorithms.

    Main Results:

    • SICOR demonstrated superior performance compared to existing methods in distinguishing RNA secondary structures.
    • The method effectively quantifies structural differences relevant to aptamer function.
    • SICOR's approach provides a robust framework for analyzing structural diversity.

    Conclusions:

    • SICOR offers an advanced and effective approach for RNA secondary structure comparison.
    • This method can significantly aid in the rational design and optimization of SELEX experiments.
    • SICOR's application extends to various fields requiring detailed RNA structural analysis.