ArticleNucleic acids research2016
RNAlien - Unsupervised RNA family model construction.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- The Historical Evolution and Significance of Multiple Sequence Alignment in Molecular Structure and Function Prediction.Biomolecules · 2024Review
- DecoyFinder: Identification of Contaminants in Sets of Homologous RNA Sequences.bioRxiv : the preprint server for biology · 2024Article
- The long noncoding RNAScience advances · 2022Article
- Getting to the bottom of lncRNA mechanism: structure-function relationships.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Review
- Rfam 14: expanded coverage of metagenomic, viral and microRNA families.Nucleic acids research · 2021Article
- The RNA workbench 2.0: next generation RNA data analysis.Nucleic acids research · 2019Article
- CMV: visualization for RNA and protein family models and their comparisons.Bioinformatics (Oxford, England) · 2018Article
- Freiburg RNA tools: a central online resource for RNA-focused research and teaching.Nucleic acids research · 2018Article
- Structure and Interaction Prediction in Prokaryotic RNA Biology.Microbiology spectrum · 2018Review
- A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs.Nucleic acids research · 2018Article
- StructRNAfinder: an automated pipeline and web server for RNA families prediction.BMC bioinformatics · 2018Article
- GLASSgo - Automated and Reliable Detection of sRNA Homologs From a Single Input Sequence.Frontiers in genetics · 2018Article
- The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.Nucleic acids research · 2017Article
- Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops.RNA (New York, N.Y.) · 2017Article
- RNAcentral: a comprehensive database of non-coding RNA sequences.Nucleic acids research · 2017Article
- Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs.Frontiers in microbiology · 2017Review
- The Transcriptome ofFrontiers in cellular and infection microbiology · 2016Article
Corrections and comments
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Authors and funding
3 authors.
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Abstract
Determining the function of a non-coding RNA requires costly and time-consuming wet-lab experiments. For this reason, computational methods which ascertain the homology of a sequence and thereby deduce functionality and family membership are often exploited. In this fashion, newly sequenced genomes can be annotated in a completely computational way. Covariance models are commonly used to assign novel RNA sequences to a known RNA family. However, to construct such models several examples of the family have to be already known. Moreover, model building is the work of experts who manually edit the necessary RNA alignment and consensus structure. Our method, RNAlien, starting from a single input sequence collects potential family member sequences by multiple iterations of homology search. RNA family models are fully automatically constructed for the found sequences. We have tested our method on a subset of the Rfam RNA family database. RNAlien models are a starting point to construct models of comparable sensitivity and specificity to manually curated ones from the Rfam database. RNAlien Tool and web server are available at http://rna.tbi.univie.ac.at/rnalien/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.