title: GRASP-DNA: a web application to screen prokaryotic genomes for specific DNA-binding sites and repeat motifs.
abstract: The ability to control multiple genes at the transcriptional level often relies on the existence of short stretches of well-defined DNA sequences, to which regulatory proteins and transcription factors bind. In this article we present a freely accessible web-based application (GRASP-DNA), that can be used to screen prokaryotic genomes for putative DNA-binding sites of a particular transcription factor or DNA-binding molecule. This application utilizes existing theories, such as information and statistical-mechanical theories, for the calculation of positive weight matrices generated from block aligned binding sites. Using these position weight matrices entire prokaryotic genomes are screened to identify sites that display a high level of sequence similarity to existing binding sites. This application can be used in combination with high-throughput technologies for gene expression analysis and binding site characterization to assist in the elucidation of global regulatory networks.
authors.affiliation: Deparment of Bioengineering University of California, San Diego, La Jolla 92093-0412, USA. cschilli@bioeng.ucsd.edu
authors.forename: C H
authors.initials: CH
authors.lastname: Schilling
authors.forename: L
authors.initials: L
authors.lastname: Held
authors.forename: M
authors.initials: M
authors.lastname: Torre
authors.forename: M H
authors.initials: MH
authors.lastname: Saier
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D020407:Internet; D012045:Regulatory Sequences, Nucleic Acid; D016415:Sequence Alignment; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D014157:Transcription Factors; D004247:DNA