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.

paste a one word query
name of protein or DNA sequence ?




How the miner works

Abstracts 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,upstream
Get in touch if you want the Perl source code of the consensus miner to run it in your own computer.

Links to related resources