ArticleBioinformatics (Oxford, England)2012
CodonLogo: a sequence logo-based viewer for codon patterns.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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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.
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Who cites it
9 citing papers in PubMed, 20 citations in OpenAlex.
- A single amino acid in the viral capsid makes a major contribution to the interaction between human norovirus GII.6 and the bacterial Psl exopolysaccharide.Applied and environmental microbiology · 2026Article
- Molecular Characterization and Expression ofAnimals : an open access journal from MDPI · 2025Article
- plotnineSeqSuite: a Python package for visualizing sequence data using ggplot2 style.BMC genomics · 2023Article
- CoCoView - A codon conservation viewer via sequence logos.MethodsX · 2022Article
- Logomaker: beautiful sequence logos in Python.Bioinformatics (Oxford, England) · 2020Article
- Examination of the Glycine Betaine-Dependent Methylotrophic Methanogenesis Pathway: Insights Into Anaerobic Quaternary Amine Methylotrophy.Frontiers in microbiology · 2019Article
- Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs.BMC proceedings · 2014Article
- 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
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
motivationConserved patterns across a multiple sequence alignment can be visualized by generating sequence logos. Sequence logos show each column in the alignment as stacks of symbol(s) where the height of a stack is proportional to its informational content, whereas the height of each symbol within the stack is proportional to its frequency in the column. Sequence logos use symbols of either nucleotide or amino acid alphabets. However, certain regulatory signals in messenger RNA (mRNA) act as combinations of codons. Yet no tool is available for visualization of conserved codon patterns.
resultsWe present the first application which allows visualization of conserved regions in a multiple sequence alignment in the context of codons. CodonLogo is based on WebLogo3 and uses the same heuristics but treats codons as inseparable units of a 64-letter alphabet. CodonLogo can discriminate patterns of codon conservation from patterns of nucleotide conservation that appear indistinguishable in standard sequence logos. AVAILABILITY: The CodonLogo source code and its implementation (in a local version of the Galaxy Browser) are available at http://recode.ucc.ie/CodonLogo and through the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/.
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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.