ArticleNucleic acids research2006
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- SARS-CoV-2 3CLpro whole human proteome cleavage prediction and enrichment/depletion analysis.Computational biology and chemistry · 2022Article
- Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences.PloS one · 2019Article
- CircularLogo: A lightweight web application to visualize intra-motif dependencies.BMC bioinformatics · 2017Article
- RNA Thermodynamic Structural Entropy.PloS one · 2015Article
- ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos.BMC proceedings · 2014Article
- BlockLogo: visualization of peptide and sequence motif conservation.Journal of immunological methods · 2013Article
- Computational detection of abundant long-range nucleotide covariation in Drosophila genomes.RNA (New York, N.Y.) · 2013Article
- CodonLogo: a sequence logo-based viewer for codon patterns.Bioinformatics (Oxford, England) · 2012Article
- 70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence.Nucleic acids research · 2010Article
- A brief review of molecular information theory.Nano communication networks · 2010Article
- Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE.BMC research notes · 2008Article
- RNALogo: a new approach to display structural RNA alignment.Nucleic acids research · 2008Article
- MetaLook: a 3D visualisation software for marine ecological genomics.BMC bioinformatics · 2007Article
- RADAR: a web server for RNA data analysis and research.Nucleic acids research · 2007Article
- Incorporating background frequency improves entropy-based residue conservation measures.BMC bioinformatics · 2006Article
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Authors and funding
3 authors.
Funding
Abstract
We present an online server that generates a 3D representation of properties of user-submitted RNA or DNA alignments. The visualized properties are information of single alignment columns, mutual information of two alignment positions as well as the position-specific fraction of gaps. The nucleotide composition of both single columns and column pairs is visualized with the help of color-coded 3D bars labeled with letters. The server generates both VRML and JVX output that can be viewed with a VRML viewer or the JavaView applet, respectively. We show that combining these different features of an alignment into one 3D representation is helpful in identifying correlations between bases and potential RNA and DNA base pairs. Significant known correlations between the tRNA 3' anticodon cardinal nucleotide and the extended anticodon were observed, as were correlations within the amino acid acceptor stem and between the cardinal nucleotide and the acceptor stem. The online server can be accessed using the URL http://correlogo.abcc.ncifcrf.gov.
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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.