title: DMINDA: an integrated web server for DNA motif identification and analyses.
abstract: DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular.
authors.affiliation: Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens GA 30602, USA BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA.
authors.forename: Qin
authors.initials: Q
authors.lastname: Ma
authors.affiliation: Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens GA 30602, USA College of Computer Science and Technology, Jilin University, Changchun, China.
authors.forename: Hanyuan
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens GA 30602, USA BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA.
authors.forename: Xizeng
authors.initials: X
authors.lastname: Mao
authors.affiliation: School of Mathematics, Shandong University, Jinan, Shandong, China.
authors.forename: Chuan
authors.initials: C
authors.lastname: Zhou
authors.affiliation: School of Mathematics, Shandong University, Jinan, Shandong, China.
authors.forename: Bingqiang
authors.initials: B
authors.lastname: Liu
authors.affiliation: Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens GA 30602, USA College of Computer Science and Technology, Jilin University, Changchun, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Chen
authors.affiliation: Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens GA 30602, USA BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA College of Computer Science and Technology, Jilin University, Changchun, China xyn@bmb.uga.edu.
authors.forename: Ying
authors.initials: Y
authors.lastname: Xu
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D020407:Internet; D059372:Nucleotide Motifs; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA; D012984:Software; D018511:Systems Integration; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors; D004247:DNA
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