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HSEAT: A Tool for Plant Heat Shock Element Analysis, Motif Identification and Analysis


Sarah Rizwan Qazi, Noor ul Haq, Shakeel Ahmad and Samina N Shakeel*  


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 Chloroplast specific small heat shock proteins (Cp-sHSPs) creation is correlated with plant tolerance under heat and other stress conditions. Regulation of these Cp-sHSP 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 sHSP genes is because of their unique promoter architecture, cis-acting sequences and their interaction with HSFs.

We present here a versatile promoter analysis tool for identification and analysis of promoters of Cp-sHSPs. Heat Shock Element Analysis Tool (HSEAT) was designed to detect different types of HSEs in promoter regions of plant Cp-sHSPs 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 sHSPs as described recently [1-2]. Here we examined and evaluated some known Cp-sHSP promoters from different plants using this tool with already available tools.

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


Heat Shock Element, Heat Shock Proteins, Plants, Heat Stress


Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University 45320, Islamabad, Department of Computer Science and BioInformatics, Khushal Khan Khattak University 27200, Karak, Khyber-Pakhtunkhwa, Pakistan Institute of Science and Technology (PINSTECH), Nilore, Islamabad, Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University 45320, Islamabad

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