ArticleNucleic acids research2008
RNALogo: a new approach to display structural RNA alignment.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed, 50 citations in OpenAlex.
- Molecular characterization of miRNA genes and their expression in Dimocarpus longan Lour.Planta · 2021Article
- Delimitation of five astome ciliate species isolated from the digestive tube of three ecologically different groups of lumbricid earthworms, using the internal transcribed spacer region and the hypervariable D1/D2 region of the 28S rRNA gene.BMC evolutionary biology · 2020Article
- dagLogo: An R/Bioconductor package for identifying and visualizing differential amino acid group usage in proteomics data.PloS one · 2020Article
- Phylogenetic analysis of Uncaria species based on internal transcribed spacer (ITS) region and ITS2 secondary structure.Pharmaceutical biology · 2018Article
- Expression and function of microRNA-9 in the mid-hindbrain area of embryonic chick.BMC developmental biology · 2018Article
- The sRNAome mining revealed existence of unique signature small RNAs derived from 5.8SrRNA from Piper nigrum and other plant lineages.Scientific reports · 2017Article
- Unravelling the complexity of microRNA-mediated gene regulation in black pepper (Piper nigrum L.) using high-throughput small RNA profiling.Plant cell reports · 2016Article
- The iceLogo web server and SOAP service for determining protein consensus sequences.Nucleic acids research · 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
- Candidate RNA structures for domain 3 of the foot-and-mouth-disease virus internal ribosome entry site.Nucleic acids research · 2013Article
- An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs.BMC bioinformatics · 2013Article
- A small ribozyme with dual-site kinase activity.Nucleic acids research · 2012Article
- CodonLogo: a sequence logo-based viewer for codon patterns.Bioinformatics (Oxford, England) · 2012Article
- MapMi: automated mapping of microRNA loci.BMC bioinformatics · 2010Article
- miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression.BMC bioinformatics · 2009Article
- Detecting species-site dependencies in large multiple sequence alignments.Nucleic acids research · 2009Article
- Article
- Computational identification of riboswitches based on RNA conserved functional sequences and conformations.RNA (New York, N.Y.) · 2009Article
- sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes.Nucleic acids research · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Regulatory RNAs play essential roles in many essential biological processes, ranging from gene regulation to protein synthesis. This work presents a web-based tool, RNALogo, to create a new graphical representation of the patterns in a multiple RNA sequence alignment with a consensus structure. The RNALogo graph can indicate significant features within an RNA sequence alignment and its consensus RNA secondary structure. RNALogo extends Sequence logos, and specifically incorporates RNA secondary structures and mutual information of base-paired regions into the graphical representation. Each RNALogo graph is composed of stacks of letters, with one stack for each position in the consensus RNA secondary structure. RNALogo provides a convenient and high configurable logo generator. An RNALogo graph is generated for each RNA family in Rfam, and these generated logos are accumulated into a gallery of RNALogo. Users can search or browse RNALogo graphs in this gallery to receive additional perspectives of known RNA families. RNALogo is now available at: http://rnalogo.mbc.nctu.edu.tw/.
Indexed as
Identifiers
What OpenQuestion holds
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.