The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
RNA sequence analysis using covariance models
Open accessAbstract
We describe a general approach to several RNA sequence analysis problems using probabilistic models that flexibly describe the secondary structure and primary sequence consensus of an RNA sequence family. We call these models 'covariance models'. A covariance model of tRNA sequences is an extremely sensitive and discriminative tool for searching for additional tRNAs and tRNA-related sequences in sequence databases. A model can be built automatically from an existing sequence alignment. We also describe an algorithm for learning a model and hence a consensus secondary structure from initially unaligned example sequences and no prior structural information. Models trained on unaligned tRNA examples correctly predict tRNA secondary structure and produce high-quality multiple alignments. The approach may be applied to any family of small RNA sequences.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
Encoded combinatorial chemistry.
Brenner, S., & Lerner, R. A. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.12.5381 · Cited by 1,014
Isolation of New Ribozymes from a Large Pool of Random Sequences
Bartel, D. P., & Szostak, J. W. (1993) · Science · doi:10.1126/science.7690155 · Cited by 900
Cited by
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes
Chan, P. P., Lin, B. Y., Mak, A. J., & Lowe, T. M. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab688 · Cited by 1,925
Targeting RNA structures with small molecules
Childs-Disney, J. L., Yang, X., Gibaut, Q. M. R., Tong, Y., Batey, R. T., & Disney, M. D. (2022) · Nature Reviews Drug Discovery · doi:10.1038/s41573-022-00521-4 · Cited by 587
Identification of a target RNA motif for RNA-binding protein HuR
de Silanes, I. L., Zhan, M., Lal, A., Yang, X., & Gorospe, M. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0306453101 · Cited by 502
RNA Pseudoknot Prediction in Energy-Based Models
Lyngsø, R. B., & Pedersen, C. N. S. (2000) · Journal of Computational Biology · doi:10.1089/106652700750050862 · Cited by 359
Weinberg, Z., Wang, J. X., Bogue, J., Yang, J., Corbino, K., Moy, R. H., & Breaker, R. R. (2010) · Genome Biology · doi:10.1186/gb-2010-11-3-r31 · Cited by 354
Metadata
- Authors
- Eddy, S. R., & Durbin, R.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 1994
- Volume
- 22
- Issue
- 11
- Pages
- 2079-2088
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2011368877
- Cited by
- 793
- References
- 4
- FWCI
- 3.80
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: RNA sequence analysis using covariance models. https://app.cochat.ai/papers/10.1093/nar/22.11.2079
- The paper
- Eddy, S. R., & Durbin, R. (1994). RNA sequence analysis using covariance models. Nucleic Acids Research. https://doi.org/10.1093/nar/22.11.2079
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
