04/04/2014, the paper of DMINDA server has been accepted by Nucleic Acids Research.
DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses. This website is freely available to all users and there is no login requirement. This server provides a suite of cis regulatory DNA motif analysis functions, which are important to elucidating the mechanism of transcriptional regulation:
(i) de novo motif finding for a given set of promoter sequences along with motif evaluation based on information extracted from a control set or a set of reference genomes;
(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 DNA-motif 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.
Please cites the following papers if you use the result of the motif finding program:
1.Qin Ma*, Hanyuan Zhang*, Xizeng Mao, Chuan Zhou, Bingqiang Liu, Xin Chen, Ying Xu, DMINDA: An integrated web server for DNA motif identification and analyses, Nucleic Acids Research, doi: 10.1093/nar/gku315, 2014.  (PMID:24753419).
2. Qin Ma, Bingqiang Liu, Chuan Zhou, Yanbin Yin, Guojun Li, Ying Xu, BoBro2.0: An integrated toolkit for accurate prediction and analysis of cis regulatory elements at a genome scale. Bioinformatics, 10.1093/bioinformatics/btt397, 2013 (PMID:23846744)
3. Guojun Li, Bingqiang Liu, Qin Ma, Ying Xu, A new framework for identifying cis-regulatory motifs in prokaryotes, Nucleic Acids Research. 2011 Apr;39(7):e42 (PMID:21149261)
4. Guojun. Li*,Bingqiang Liu*, Ying Xu, Accurate Recognition of cis Regulatory Motifs with the Correct Lengths in Prokaryotic Genomes, Nucleic Acids Research, Vol. 38, No. 2, e12, 2010. (PMID:19906734)