A comprehensive comparison of comparative RNA structure prediction approaches

An increasing number of researchers have released novel RNA structure analysis and prediction algorithms for comparative approaches to structure prediction. Yet, independent benchmarking of these algorithms is rarely performed as is now common practice for protein-folding, gene-finding and multiple-...

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Bibliographic Details
Published inBMC bioinformatics Vol. 5; no. 1; p. 140
Main Authors Gardner, Paul P, Giegerich, Robert
Format Journal Article
LanguageEnglish
Published England BioMed Central Ltd 30.09.2004
BioMed Central
BMC
Subjects
Algorithms
Benchmarking - methods
Consensus Sequence - genetics
Escherichia coli K12 - genetics
Nucleic Acid Conformation
Predictive Value of Tests
RNA - genetics
RNA, Bacterial - genetics
RNA, Fungal
Saccharomyces cerevisiae - genetics
Sequence Alignment - methods
Software
Software Design
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Summary:An increasing number of researchers have released novel RNA structure analysis and prediction algorithms for comparative approaches to structure prediction. Yet, independent benchmarking of these algorithms is rarely performed as is now common practice for protein-folding, gene-finding and multiple-sequence-alignment algorithms. Here we evaluate a number of RNA folding algorithms using reliable RNA data-sets and compare their relative performance. We conclude that comparative data can enhance structure prediction but structure-prediction-algorithms vary widely in terms of both sensitivity and selectivity across different lengths and homologies. Furthermore, we outline some directions for future research.
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ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-5-140