Predicts transcription factor (TF) binding targets and cis-regulatory modules (CRM), based on motifs representing experimentally determined DNA binding specificities. Genome Surveyor displays genome browser tracks that profile matches to individual motifs or user-selected combinations of motifs, based on sequence information from a single genome or a combination of genomes. It also provides tracks for supervised CRM prediction, driven by a user-selected subset of known CRMs from the REDfly database. Users select the type of binding site profiles that will be used for search. Next, they may choose to scan the entire genome, or provide a list of genomic loci where the search will be performed.
Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
Genome Surveyor funding source(s)
This work was supported in part by grants by the National Institute of Health (grant R01HG004744-01, grant R01GM085233-01).