ArticleRNA (New York, N.Y.)2009
The RNA structure alignment ontology.
Article in RNA (New York, N.Y.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- RNAhub-an automated pipeline to search and align RNA homologs with secondary structure assessment.Nucleic acids research · 2025Article
- DecoyFinder: Identification of Contaminants in Sets of Homologous RNA Sequences.bioRxiv : the preprint server for biology · 2024Article
- JACALIN-LECTIN LIKE1 Regulates the Nuclear Accumulation of GLYCINE-RICH RNA-BINDING PROTEIN7, Influencing the RNA Processing of FLOWERING LOCUS C Antisense Transcripts and Flowering Time in Arabidopsis.Plant physiology · 2015Article
- Ambivalent covariance models.BMC bioinformatics · 2015Article
- Aptamer Selection Technology and Recent Advances.Molecular therapy. Nucleic acids · 2015Review
- R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.Nucleic acids research · 2013Article
- Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch.Journal of molecular biology · 2013Article
- An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with transcripts in Arabidopsis thaliana.Nucleic acids research · 2012Article
- RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs.RNA (New York, N.Y.) · 2012Article
- rCAD: A Novel Database Schema for the Comparative Analysis of RNA.Proceedings ... IEEE International Conference on eScience. IEEE International Conference on eScience · 2011Article
- Sharing and archiving nucleic acid structure mapping data.RNA (New York, N.Y.) · 2011Article
- Boulder ALignment Editor (ALE): a web-based RNA alignment tool.Bioinformatics (Oxford, England) · 2011Article
- Meeting report of the RNA Ontology Consortium January 8-9, 2011.Standards in genomic sciences · 2011Article
- TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences.BMC bioinformatics · 2011Article
- Nuclear and cytoplasmic localization of neural stem cell microRNAs.RNA (New York, N.Y.) · 2011Article
- Predicting and modeling RNA architecture.Cold Spring Harbor perspectives in biology · 2011Review
- Rfam: Wikipedia, clans and the "decimal" release.Nucleic acids research · 2011Article
- Spotlight on post-transcriptional control in the circadian system.Cellular and molecular life sciences : CMLS · 2011Review
- Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities?The journal of physical chemistry. B · 2010Article
- R3D Align: global pairwise alignment of RNA 3D structures using local superpositions.Bioinformatics (Oxford, England) · 2010Article
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Multiple sequence alignments are powerful tools for understanding the structures, functions, and evolutionary histories of linear biological macromolecules (DNA, RNA, and proteins), and for finding homologs in sequence databases. We address several ontological issues related to RNA sequence alignments that are informed by structure. Multiple sequence alignments are usually shown as two-dimensional (2D) matrices, with rows representing individual sequences, and columns identifying nucleotides from different sequences that correspond structurally, functionally, and/or evolutionarily. However, the requirement that sequences and structures correspond nucleotide-by-nucleotide is unrealistic and hinders representation of important biological relationships. High-throughput sequencing efforts are also rapidly making 2D alignments unmanageable because of vertical and horizontal expansion as more sequences are added. Solving the shortcomings of traditional RNA sequence alignments requires explicit annotation of the meaning of each relationship within the alignment. We introduce the notion of "correspondence," which is an equivalence relation between RNA elements in sets of sequences as the basis of an RNA alignment ontology. The purpose of this ontology is twofold: first, to enable the development of new representations of RNA data and of software tools that resolve the expansion problems with current RNA sequence alignments, and second, to facilitate the integration of sequence data with secondary and three-dimensional structural information, as well as other experimental information, to create simultaneously more accurate and more exploitable RNA alignments.
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