Background: Previous methods used to discover cis-regulatory motifs in promoter
region of plant genes possess very limited performance, especially for analysis of novel and rare
motifs. Different plant genes have differential expression under different environmental or
experimental conditions and modular regulation of cis-regulatory sequences in promoter regions of
the same or different genes. It has previously been revealed that Heat Shock Proteins (HSPs)
creation is correlated with plant tolerance under heat and other stress conditions. Regulation of
these HSP genes is controlled by interactions between heat shock factors (HSFs) with cis-acting
motifs present in the promoter region of the genes. Differential expression of these HSP genes is
because of their unique promoter architecture, cis-acting sequences and their interaction with
Objective: A versatile promoter analysis tool was proposed for identification and analysis of
promoters of HSPs.
Methods: Heat Shock Element Analysis Tool (HSEAT) has been implemented in java
programming language using pattern recognition approach. This tool has build-in MS access
database for storing different motifs.
Results: HSEAT has been designed to detect different types of Heat Shock Elements (HSEs) in
promoter regions of plant HSPs with integration of complete analysis of plant promoters to the
tool. HSEAT is user-friendly, interactive application to discover various types of HSEs e.g. TTC
Rich Types, Gap Types and Prefect HSE as well as STRE in HSPs. Here we examined and
evaluated some known HSP promoters from different plants using this tool with already available
Conclusion: HSEAT has extensive potential to explore conserved or semi-conserved motifs or
potential binding sites of different transcription factors for other stress regulating genes. This tool
can be found at https://sourceforge.net/projects/heast/.