{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Gordan R"],"funding":["NIEHS NIH HHS","NHLBI NIH HHS","NIGMS NIH HHS"],"pagination":["e90"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC2847231"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["38(6)"],"pubmed_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"],"journal":["Nucleic acids research"],"pubmed_title":["Finding regulatory DNA motifs using alignment-free evolutionary conservation information."],"pmcid":["PMC2847231"],"funding_grant_id":["HR0011-09-1-0040","P50-GM081883-01","HR0011-08-1-0023","R01-ES015165-01"],"pubmed_authors":["Gordan R","Hartemink AJ","Narlikar L"],"additional_accession":[]},"is_claimable":false,"name":"Finding regulatory DNA motifs using alignment-free evolutionary conservation information.","description":"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","dates":{"release":"2010-01-01T00:00:00Z","publication":"2010 Apr","modification":"2025-04-04T19:35:04.912Z","creation":"2019-03-27T00:29:46Z"},"accession":"S-EPMC2847231","cross_references":{"pubmed":["20047961"],"doi":["10.1093/nar/gkp1166"]}}