ArticleBMC bioinformatics2010
Fine-tuning structural RNA alignments in the twilight zone.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.Briefings in bioinformatics · 2023Review
- Graph Theory-Based Sequence Descriptors as Remote Homology Predictors.Biomolecules · 2019Article
- aliFreeFold: an alignment-free approach to predict secondary structure from homologous RNA sequences.Bioinformatics (Oxford, England) · 2018Article
- The BRaliBase dent-a tale of benchmark design and interpretation.Briefings in bioinformatics · 2017Article
- Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores.BMC bioinformatics · 2015Article
- Widespread purifying selection on RNA structure in mammals.Nucleic acids research · 2013Article
- Detecting and comparing non-coding RNAs in the high-throughput era.International journal of molecular sciences · 2013Review
- Structator: fast index-based search for RNA sequence-structure patterns.BMC bioinformatics · 2011Article
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3 authors.
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Abstract
backgroundA widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably.
resultsBased on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices.
conclusionsEmploying the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index.
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