This miner allows you to search for DNA sequences included in literature abstracts, such as consensus signatures or binding sites.
WARNING: Jobs take around a minute to complete, as queries to PubMed Entrez servers are spaced to prevent overloads. You might have to re-send queries or try a mirror server as jobs might fail depending on web traffic.
How the miner worksAbstracts are retrieved from PubMed using a tailored set of keywords, some provided by A.Santos-Zavaleta (curator at RegulonDB/EcoCyc) and some found to be overrepresented in abstracts of papers curated at RegulonDB (Escherichia coli articles) and TRANSFAC (papers about eukaryotic transcriptional regulation). These keywords are:
binding site,chip,chromatin,consensus,element,footprinting,identified,logo, matrix,motif,mutagenesis,mutation,operator,promoter,regulatory,restriction, site,selex,sequence,shift,site-specific,specificity,target,transcription,upstreamGet in touch if you want the Perl source code of the consensus miner to run it in your own computer.