DMINDA: an integrated web server for DNA motif identification and analyses

Qin Ma; Hanyuan Zhang; Xizeng Mao; Chuan Zhou; Bingqiang Liu; Xin Chen; Ying Xu

doi:10.1093/nar/gku315

DMINDA: an integrated web server for DNA motif identification and analyses

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W12-9. doi: 10.1093/nar/gku315. Epub 2014 Apr 21.

Authors

Qin Ma¹, Hanyuan Zhang², Xizeng Mao¹, Chuan Zhou³, Bingqiang Liu³, Xin Chen², Ying Xu⁴

Affiliations

¹ 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.
² 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.
³ School of Mathematics, Shandong University, Jinan, Shandong, China.
⁴ 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.

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.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Binding Sites
DNA / chemistry*
Internet
Nucleotide Motifs
Promoter Regions, Genetic*
Sequence Analysis, DNA
Software*
Systems Integration
Transcription Factors / metabolism

Substances

Transcription Factors
DNA