ArticleBMC bioinformatics2007
WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
- Identification of upstream transcription factor binding sites in orthologous genes using mixed Student's t-test statistics.PLoS computational biology · 2022Article
- Maser: one-stop platform for NGS big data from analysis to visualization.Database : the journal of biological databases and curation · 2018Article
- Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species.BMC developmental biology · 2015Article
- iRegulon: from a gene list to a gene regulatory network using large motif and track collections.PLoS computational biology · 2014Article
- A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data.Biology direct · 2014Review
- Nitrogen transporter and assimilation genes exhibit developmental stage-selective expression in maize (Zea mays L.) associated with distinct cis-acting promoter motifs.Plant signaling & behavior · 2013Article
- Molecular cloning of doublesex genes of four cladocera (water flea) species.BMC genomics · 2013Article
- Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas.BMC plant biology · 2013Article
- ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites.Bioinformatics (Oxford, England) · 2012Article
- Molecular mechanisms of EGF signaling-dependent regulation of pipe, a gene crucial for dorsoventral axis formation in Drosophila.Development genes and evolution · 2012Article
- A mutation degree model for the identification of transcriptional regulatory elements.BMC bioinformatics · 2011Article
- MotifClick: prediction of cis-regulatory binding sites via merging cliques.BMC bioinformatics · 2011Article
- Exhaustive search for over-represented DNA sequence motifs with CisFinder.DNA research : an international journal for rapid publication of reports on genes and genomes · 2009Article
- Promoter analysis: gene regulatory motif identification with A-GLAM.Methods in molecular biology (Clifton, N.J.) · 2009Article
- Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation.BMC bioinformatics · 2008Article
- MTAP: the motif tool assessment platform.BMC bioinformatics · 2008Article
- Conserved upstream open reading frames in higher plants.BMC genomics · 2008Article
- The low temperature-responsive, Solanum CBF1 genes maintain high identity in their upstream regions in a genomic environment undergoing gene duplications, deletions, and rearrangements.Plant molecular biology · 2008Article
- Genomic organization and evolutionary conservation of plant D-type cyclins.Plant physiology · 2007Article
- Review of Different Sequence Motif Finding Algorithms.Avicenna journal of medical biotechnologyReview
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3 authors.
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Abstract
backgroundThis work addresses the problem of detecting conserved transcription factor binding sites and in general regulatory regions through the analysis of sequences from homologous genes, an approach that is becoming more and more widely used given the ever increasing amount of genomic data available.
resultsWe present an algorithm that identifies conserved transcription factor binding sites in a given sequence by comparing it to one or more homologs, adapting a framework we previously introduced for the discovery of sites in sequences from co-regulated genes. Differently from the most commonly used methods, the approach we present does not need or compute an alignment of the sequences investigated, nor resorts to descriptors of the binding specificity of known transcription factors. The main novel idea we introduce is a relative measure of conservation, assuming that true functional elements should present a higher level of conservation with respect to the rest of the sequence surrounding them. We present tests where we applied the algorithm to the identification of conserved annotated sites in homologous promoters, as well as in distal regions like enhancers.
conclusionResults of the tests show how the algorithm can provide fast and reliable predictions of conserved transcription factor binding sites regulating the transcription of a gene, with better performances than other available methods for the same task. We also show examples on how the algorithm can be successfully employed when promoter annotations of the genes investigated are missing, or when regulatory sites and regions are located far away from the genes.
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