ArticleNucleic acids research2010
Finding regulatory DNA motifs using alignment-free evolutionary conservation information.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 51 citations in OpenAlex.
- Inferring fungal cis-regulatory networks from genome sequences via unsupervised and interpretable representation learning.Genetics · 2026Article
- Species-aware DNA language models capture regulatory elements and their evolution.Genome biology · 2024Article
- Precise temporal control of neuroblast migration through combined regulation and feedback of a Wnt receptor.eLife · 2023Article
- Deep Conservation ofThe Plant cell · 2019Article
- A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome.PLoS computational biology · 2018Article
- Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi.eLife · 2016Article
- BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements.Bioinformatics (Oxford, England) · 2015Article
- Identification and computational analysis of gene regulatory elements.Cold Spring Harbor protocols · 2015Review
- Article
- TargetOrtho: a phylogenetic footprinting tool to identify transcription factor targets.Genetics · 2014Article
- Identification of functional cis-regulatory elements by sequential enrichment from a randomized synthetic DNA library.BMC plant biology · 2013Article
- One size does not fit all: on how Markov model order dictates performance of genomic sequence analyses.Nucleic acids research · 2013Article
- MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis.BMC bioinformatics · 2013Article
- MuMoD: a Bayesian approach to detect multiple modes of protein-DNA binding from genome-wide ChIP data.Nucleic acids research · 2013Article
- P-value-based regulatory motif discovery using positional weight matrices.Genome research · 2013Article
- The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences.Nucleic acids research · 2012Article
- Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs.Nucleic acids research · 2012Article
- Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity.Development (Cambridge, England) · 2012Article
- Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts.Bioinformatics (Oxford, England) · 2012Article
- Epigenetic priors for identifying active transcription factor binding sites.Bioinformatics (Oxford, England) · 2012Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
As an increasing number of eukaryotic genomes are being sequenced, comparative studies aimed at detecting regulatory elements in intergenic sequences are becoming more prevalent. Most comparative methods for transcription factor (TF) binding site discovery make use of global or local alignments of orthologous regulatory regions to assess whether a particular DNA site is conserved across related organisms, and thus more likely to be functional. Since binding sites are usually short, sometimes degenerate, and often independent of orientation, alignment algorithms may not align them correctly. Here, we present a novel, alignment-free approach for using conservation information for TF binding site discovery. We relax the definition of conserved sites: we consider a DNA site within a regulatory region to be conserved in an orthologous sequence if it occurs anywhere in that sequence, irrespective of orientation. We use this definition to derive informative priors over DNA sequence positions, and incorporate these priors into a Gibbs sampling algorithm for motif discovery. Our approach is simple and fast. It requires neither sequence alignments nor the phylogenetic relationships between the orthologous sequences, yet it is more effective on real biological data than methods that do.
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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.