ArticleBMC bioinformatics2008
Strategies for measuring evolutionary conservation of RNA secondary structures.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
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- Genetic robustness of let-7 miRNA sequence-structure pairs.RNA (New York, N.Y.) · 2019Article
- A threonyl-tRNA synthetase-mediated translation initiation machinery.Nature communications · 2019Article
- Next-Generation Sequencing of the Complete Mitochondrial Genome of the Endangered Species Black Lion TamarinG3 (Bethesda, Md.) · 2018Article
- DotAligner: identification and clustering of RNA structure motifs.Genome biology · 2017Article
- PARTICLE triplexes cluster in the tumor suppressor WWOX and may extend throughout the human genome.Scientific reports · 2017Article
- Recognizing RNA structural motifs in HT-SELEX data for ribosomal protein S15.BMC bioinformatics · 2017Article
- Genome-scale characterization of RNA tertiary structures and their functional impact by RNA solvent accessibility prediction.RNA (New York, N.Y.) · 2017Article
- Identification and characterization of new isoforms of human fas apoptotic inhibitory molecule (FAIM).PloS one · 2017Article
- Evolution of microRNA in primates.PloS one · 2017Article
- Article
- RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory.BMC bioinformatics · 2016Article
- Analysis of 5' gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals.BMC evolutionary biology · 2015Article
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4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEvolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. Since almost all of the available methods used for prediction and annotation of non-coding RNA genes rely on this evolutionary signature, accurate measures for structural conservation are essential.
resultsWe systematically assessed the ability of various measures to detect conserved RNA structures in multiple sequence alignments. We tested three existing and eight novel strategies that are based on metrics of folding energies, metrics of single optimal structure predictions, and metrics of structure ensembles. We find that the folding energy based SCI score used in the RNAz program and a simple base-pair distance metric are by far the most accurate. The use of more complex metrics like for example tree editing does not improve performance. A variant of the SCI performed particularly well on highly conserved alignments and is thus a viable alternative when only little evolutionary information is available. Surprisingly, ensemble based methods that, in principle, could benefit from the additional information contained in sub-optimal structures, perform particularly poorly. As a general trend, we observed that methods that include a consensus structure prediction outperformed equivalent methods that only consider pairwise comparisons.
conclusionStructural conservation can be measured accurately with relatively simple and intuitive metrics. They have the potential to form the basis of future RNA gene finders, that face new challenges like finding lineage specific structures or detecting mis-aligned sequences.
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