ExactSearch: a web-based plant motif search tool

BACKGROUND: Plant biologists frequently need to examine if a sequence motif bound by a specific transcription or translation factor is present in the proximal promoters or 3′ untranslated regions (3′ UTR) of a set of plant genes of interest. To achieve such a task, plant biologists have to not only identify an appropriate algorithm for motif searching, but also manipulate the large volume of sequence data, making it burdensome to carry out or fulfill. RESULT: In this study, we developed a web portal that enables plant molecular biologists to search for DNA motifs especially degenerate ones in custom sequences or the flanking regions of all genes in the 50 plant species whose genomes have been sequenced. A web tool like this is demanded to meet a variety of needs of plant biologists for identifying the potential gene regulatory relationships. We implemented a suffix tree algorithm to accelerate the searching process of a group of motifs in a multitude of target genes. The motifs to be searched can be in the degenerate bases in addition to adenine (A), cytosine (C), guanine (G), and thymine (T). The target sequences to be searched can be custom sequences or the selected proximal gene sequences from any one of the 50 sequenced plant species. The web portal also contains the functionality to facilitate the search of motifs that are represented by position probability matrix in above-mentioned species. Currently, the algorithm can accomplish an exhaust search of 100 motifs in 35,000 target sequences of 2 kb long in 4.2 min. However, the runtime may change in the future depending on the space availability, number of running jobs, network traffic, data loading, and output packing and delivery through electronic mailing. CONCLUSION: A web portal was developed to facilitate searching of motifs presents in custom sequences or the proximal promoters or 3′ UTR of 50 plant species with the sequenced genomes. This web tool is accessible by using this URL: http://sys.bio.mtu.edu/motif/index.php.