ArticleRNA (New York, N.Y.)2020
RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency.
Article in RNA (New York, N.Y.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Article
- Phoronids and their tubes harbor distinct microbiomes compared to surrounding sediment.bioRxiv : the preprint server for biology · 2026Article
- Phylogenetic Analysis and Structural Evaluation ofbioRxiv : the preprint server for biology · 2026Article
- Large language models for bioinformatics.Quantitative biology (Beijing, China) · 2026Review
- Emergence and Tandem Repeat-Mediated Elongation of a Translated De Novo Open Reading Frame in Human Oncogenic RNA Gene VPS9D1-AS1 (MYU).Genome biology and evolution · 2026Article
- Bioinformatics Approaches in Noncoding RNAs Research.Experientia supplementum (2012) · 2026Review
- Accurate detection of tandem repeats exposes ubiquitous reuse of biological sequences.Nucleic acids research · 2025Article
- Predicting RNA Structure Utilizing Attention from Pretrained Language Models.Journal of chemical information and modeling · 2025Article
- Disentangling the gut microbiota of Aldabra giant tortoises of different ages and environments.PeerJ · 2025Article
- Exploring the potential of dental calculus to shed light on past human migrations in Oceania.Nature communications · 2024Article
- Interrelation of the spatial and genetic structure of tick-borne encephalitis virus, its reservoir host (Ecology and evolution · 2024Article
- Widespread exposure to SARS-CoV-2 in wildlife communities.Nature communications · 2024Article
- Metatranscriptomic Analysis Reveals Synergistic Activities of Comammox and Anammox Bacteria in Full-Scale Attached Growth Nitrogen Removal System.Environmental science & technology · 2024Article
- Dentition patterns and molecular diversity of Mastophorus muris (Gmelin, 1790) (Nematoda: Spiruroidea) support a host-associated subdivision.Parasitology research · 2024Article
- Arctic cyanobacterial mat community diversity decreases with latitude across the Canadian Arctic.FEMS microbiology ecology · 2024Article
- Evaluating the effects of mefenoxam on taxonomic and functional dynamics of nontarget fungal communities during carrot cultivation.Scientific reports · 2024Article
- Accurately clustering biological sequences in linear time by relatedness sorting.Nature communications · 2024Article
- Whole-mitogenome analysis unveils previously undescribed genetic diversity in cane toads across their invasion trajectory.Ecology and evolution · 2024Article
- Elevated methane flux in a tropical peatland post-fire is linked to depth-dependent changes in peat microbiome assembly.NPJ biofilms and microbiomes · 2024Article
- Multiple sequence alignment-based RNA language model and its application to structural inference.Nucleic acids research · 2024Article
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Abstract
The importance of noncoding RNA sequences has become increasingly clear over the past decade. New RNA families are often detected and analyzed using comparative methods based on multiple sequence alignments. Accordingly, a number of programs have been developed for aligning and deriving secondary structures from sets of RNA sequences. Yet, the best tools for these tasks remain unclear because existing benchmarks contain too few sequences belonging to only a small number of RNA families. RNAconTest (RNA consistency test) is a new benchmarking approach relying on the observation that secondary structure is often conserved across highly divergent RNA sequences from the same family. RNAconTest scores multiple sequence alignments based on the level of consistency among known secondary structures belonging to reference sequences in their output alignment. Similarly, consensus secondary structure predictions are scored according to their agreement with one or more known structures in a family. Comparing the performance of 10 popular alignment programs using RNAconTest revealed that DAFS, DECIPHER, LocARNA, and MAFFT created the most structurally consistent alignments. The best consensus secondary structure predictions were generated by DAFS and LocARNA (via RNAalifold). Many of the methods specific to noncoding RNAs exhibited poor scalability as the number or length of input sequences increased, and several programs displayed substantial declines in score as more sequences were aligned. Overall, RNAconTest provides a means of testing and improving tools for comparative RNA analysis, as well as highlighting the best available approaches. RNAconTest is available from the DECIPHER website (http://DECIPHER.codes/Downloads.html).
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