ArticlePLoS computational biology2010
The construction and use of log-odds substitution scores for multiple sequence alignment.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
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- A reinforcement learning approach to effective forecasting of pediatric hypoglycemia in diabetes I patients using an extended de Bruijn graph.Scientific reports · 2024Article
- Cell cycle-regulated ApiAP2s and parasite development: the Toxoplasma paradigm.Current opinion in microbiology · 2023Review
- A universal model of RNA.DNA:DNA triplex formation accurately predicts genome-wide RNA-DNA interactions.Briefings in bioinformatics · 2022Article
- Toxoplasma gondii AP2XII-2 Contributes to Proper Progression through S-Phase of the Cell Cycle.mSphere · 2020Article
- Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei.PLoS genetics · 2020Article
- Embracing Ambiguity in the Taxonomic Classification of Microbiome Sequencing Data.Frontiers in genetics · 2019Article
- Transcriptional repression by ApiAP2 factors is central to chronic toxoplasmosis.PLoS pathogens · 2018Article
- A Deconvolution Protocol for ChIP-Seq Reveals Analogous Enhancer Structures on the Mouse and Human Ribosomal RNA Genes.G3 (Bethesda, Md.) · 2018Article
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- Outlier detection in BLAST hits.Algorithms for molecular biology : AMB · 2018Article
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- Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations.PLoS computational biology · 2016Article
- LEON-BIS: multiple alignment evaluation of sequence neighbours using a Bayesian inference system.BMC bioinformatics · 2016Article
- Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties.PLoS computational biology · 2016Article
- Beyond the E-Value: Stratified Statistics for Protein Domain Prediction.PLoS computational biology · 2015Article
- Log-odds sequence logos.Bioinformatics (Oxford, England) · 2015Article
- Phylogenetic analysis reveals dynamic evolution of the poly(A)-binding protein gene family in plants.BMC evolutionary biology · 2014Article
- The Cryptosporidium parvum ApiAP2 gene family: insights into the evolution of apicomplexan AP2 regulatory systems.Nucleic acids research · 2014Article
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4 authors.
Funding
Abstract
Most pairwise and multiple sequence alignment programs seek alignments with optimal scores. Central to defining such scores is selecting a set of substitution scores for aligned amino acids or nucleotides. For local pairwise alignment, substitution scores are implicitly of log-odds form. We now extend the log-odds formalism to multiple alignments, using Bayesian methods to construct "BILD" ("Bayesian Integral Log-odds") substitution scores from prior distributions describing columns of related letters. This approach has been used previously only to define scores for aligning individual sequences to sequence profiles, but it has much broader applicability. We describe how to calculate BILD scores efficiently, and illustrate their uses in Gibbs sampling optimization procedures, gapped alignment, and the construction of hidden Markov model profiles. BILD scores enable automated selection of optimal motif and domain model widths, and can inform the decision of whether to include a sequence in a multiple alignment, and the selection of insertion and deletion locations. Other applications include the classification of related sequences into subfamilies, and the definition of profile-profile alignment scores. Although a fully realized multiple alignment program must rely upon more than substitution scores, many existing multiple alignment programs can be modified to employ BILD scores. We illustrate how simple BILD score based strategies can enhance the recognition of DNA binding domains, including the Api-AP2 domain in Toxoplasma gondii and Plasmodium falciparum.
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