ArticleBioinformatics (Oxford, England)2015
Log-odds sequence logos.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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.
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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
11 citing papers in PubMed.
- Article
- Molecular evolution of the members of the Snq2/Pdr18 subfamily of Pdr transporters in the Hemiascomycete yeasts.FEMS yeast research · 2025Article
- MSA Class Logos: a web server for automated sequence logo generation for user-defined sequence classes based on one multiple sequence alignment.Bioinformatics advances · 2025Article
- plotnineSeqSuite: a Python package for visualizing sequence data using ggplot2 style.BMC genomics · 2023Article
- Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors.BMC bioinformatics · 2022Article
- CTCF DNA-binding domain undergoes dynamic and selective protein-protein interactions.iScience · 2022Article
- In Silico Study of Superoxide Dismutase Gene Family in Potato and Effects of Elevated Temperature and Salicylic Acid on Gene Expression.Antioxidants (Basel, Switzerland) · 2022Article
- Logomaker: beautiful sequence logos in Python.Bioinformatics (Oxford, England) · 2020Article
- Comparative Epigenomics Reveals that RNA Polymerase II Pausing and Chromatin Domain Organization Control Nematode piRNA Biogenesis.Developmental cell · 2019Article
- ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo.Nature communications · 2015Article
- Evolution of lysine acetylation in the RNA polymerase II C-terminal domain.BMC evolutionary biology · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
motivationDNA and protein patterns are usefully represented by sequence logos. However, the methods for logo generation in common use lack a proper statistical basis, and are non-optimal for recognizing functionally relevant alignment columns.
resultsWe redefine the information at a logo position as a per-observation multiple alignment log-odds score. Such scores are positive or negative, depending on whether a column's observations are better explained as arising from relatedness or chance. Within this framework, we propose distinct normalized maximum likelihood and Bayesian measures of column information. We illustrate these measures on High Mobility Group B (HMGB) box proteins and a dataset of enzyme alignments. Particularly in the context of protein alignments, our measures improve the discrimination of biologically relevant positions. AVAILABILITY AND IMPLEMENTATION: Our new measures are implemented in an open-source Web-based logo generation program, which is available at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/logoddslogo/index.html. A stand-alone version of the program is also available from this site. CONTACT: altschul@ncbi.nlm.nih.gov SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.