ExactSearch: a web-based plant motif search tool.

Area of Science:

• Plant Molecular Biology
• Bioinformatics
• Genomics

Background:

• Plant biologists require tools to identify specific DNA sequence motifs within gene regulatory regions.
• Existing methods for motif searching in large plant genomic datasets are often burdensome and complex.

Purpose of the Study:

• To develop a user-friendly web portal for searching DNA motifs in plant genomes.
• To facilitate the identification of potential gene regulatory relationships in plants.

Main Methods:

• Implemented a suffix tree algorithm for accelerated motif searching.
• Developed a web portal to search degenerate DNA motifs and position probability matrices.
• Enabled searching within custom sequences or flanking regions of genes from 50 sequenced plant species.

Main Results:

• The web portal allows searching for degenerate DNA motifs and position probability matrices.
• The implemented algorithm can search 100 motifs in 35,000 target sequences (2kb) in approximately 4.2 minutes.
• The tool supports custom sequences and regulatory regions from 50 plant species.

Conclusions:

• A web portal has been successfully developed to aid plant biologists in motif discovery.
• The tool simplifies the identification of motifs in proximal promoters and 3' UTRs across 50 sequenced plant genomes.
• The web portal is accessible at http://sys.bio.mtu.edu/motif/index.php.