title: A suite of web-based programs to search for transcriptional regulatory motifs.
abstract: The identification of regulatory motifs is important for the study of gene expression. Here we present a suite of programs that we have developed to search for regulatory sequence motifs: (i) BioProspector, a Gibbs-sampling-based program for predicting regulatory motifs from co-regulated genes in prokaryotes or lower eukaryotes; (ii) CompareProspector, an extension to BioProspector which incorporates comparative genomics features to be used for higher eukaryotes; (iii) MDscan, a program for finding protein-DNA interaction sites from ChIP-on-chip targets. All three programs examine a group of sequences that may share common regulatory motifs and output a list of putative motifs as position-specific probability matrices, the individual sites used to construct the motifs and the location of each site on the input sequences. The web servers and executables can be accessed at http://seqmotifs.stanford.edu.
authors.affiliation: Stanford Medical Informatics, 251 Campus Drive X215, Stanford, CA 94305, USA.
authors.forename: Yueyi
authors.initials: Y
authors.lastname: Liu
authors.forename: Liping
authors.initials: L
authors.lastname: Wei
authors.forename: Serafim
authors.initials: S
authors.lastname: Batzoglou
authors.forename: Douglas L
authors.initials: DL
authors.lastname: Brutlag
authors.forename: Jun S
authors.initials: JS
authors.lastname: Liu
authors.forename: X Shirley
authors.initials: XS
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D005786:Gene Expression Regulation; D020407:Internet; D012045:Regulatory Sequences, Nucleic Acid; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors; D004247:DNA