ArticleNucleic acids research2013
RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- RBPmap: A Tool for Mapping and Predicting the Binding Sites of RNA-Binding Proteins Considering the Motif Environment.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Relative Information Gain: Shannon entropy-based measure of the relative structural conservation in RNA alignments.NAR genomics and bioinformatics · 2021Article
- rMAPS2: an update of the RNA map analysis and plotting server for alternative splicing regulation.Nucleic acids research · 2020Article
- Identification and analysis of consensus RNA motifs binding to the genome regulator CTCF.NAR genomics and bioinformatics · 2020Article
- SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data.Nucleic acids research · 2018Article
- Sequence-Based Prediction of RNA-Binding Residues in Proteins.Methods in molecular biology (Clifton, N.J.) · 2017Article
- A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications.Nucleic acids research · 2016Article
- Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements.Scientific reports · 2016Article
- Revealing protein-lncRNA interaction.Briefings in bioinformatics · 2016Review
- RNA-binding proteins in neurodegeneration: Seq and you shall receive.Trends in neurosciences · 2015Review
- Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation.Briefings in functional genomics · 2015Review
- RNA Thermodynamic Structural Entropy.PloS one · 2015Article
- High-throughput characterization of protein-RNA interactions.Briefings in functional genomics · 2015Review
- DMINDA: an integrated web server for DNA motif identification and analyses.Nucleic acids research · 2014Article
- GraphProt: modeling binding preferences of RNA-binding proteins.Genome biology · 2014Article
- CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data.Genome biology · 2014Article
- Computational Methods for CLIP-seq Data Processing.Bioinformatics and biology insights · 2014Review
- Finding the target sites of RNA-binding proteins.Wiley interdisciplinary reviews. RNAReview
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2 authors.
Funding
Abstract
RBPmotif web server (http://www.rnamotif.org) implements tools to identify binding preferences of RNA-binding proteins (RBPs). Given a set of sequences that are known to be bound and unbound by the RBP of interest, RBPmotif provides two types of analysis: (i) de novo motif finding when there is no a priori knowledge on RBP's binding preferences and (ii) analysis of structure preferences when there is a previously identified sequence motif for the RBP. De novo motif finding is performed with the previously published RNAcontext algorithm that learns discriminative motif models to identify both sequence and structure preferences. The results of this analysis include the inferred binding preferences of the RBP and the added predictive value of incorporating structure preferences. Second type of analysis investigates whether the instances of the previously identified sequence motif are enriched in a particular structure context in bound sequences, relative to its instances in unbound sequences. On completion, the results page shows the comparison of structure contexts of the motif instances between bound and unbound sequences and an assessment of statistical significance of detected preferences. In summary, RBPmotif web server enables the concurrent analysis of sequence and structure preferences of RBPs through a user-friendly interface.
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