About PPRESearch

PPRESearch is the first web program to search for PPRE elements online in the promoter region of any gene of interest.PPRESearch is developed very carefully, taking into consideration all the important parameters that are required for PPAR binding for better accuracy in searching the PPREs. The special features which make PPRESearch unique and accurate in PPRE prediction are as follows. PPRESearch searches for the PPRE repeats from the PPRE database. PPREs in the database are collected from the literature and which were shown to be experimentally validated through in vitro or in vivo binding assays. The PPRE isoform specificity, binding efficiency, pubmed id and their experimental validation assay type (in vitro or in vivo) for each PPRE as reported in the literatures are also included in the database and are displayed in output, PPRESearch allows the user to set threshold binding efficiency when searching for PPRE elements in a gene. In addition user could also search for PPREs with few mismatches from their PPRE consensus. For better user experience and understanding the PPRESearch displays the predicted promoter gene region with the mismatch nucleotide bases from its consensus in bold letters and outputs the start position of the gene promoter region. The information on PPRE isoform specificity and its corresponding binding strength helps to user to understand the PPAR isoform that can bind to it and preferences of PPARs. By this way PPRESearch implicates the preferential binding of PPARs to PPRE repeats.

                    Studies have reported that the binding strength of PPAR to DNA varies based on their matches from their flanking consensus (C(A/G)(A/G)A(A/T)CT). PPREs having greater than 4 matches from their consensus of 7 nucleotides have better binding strength to PPARs. PPRESearch searches for 5’ flanking sequence of the predicted PPRE element and displays the 5’ flanking sequence and its total number of matches from its consensus. PPRESearch also allows the user to set threshold flanking count when predicting PPRE. Other studies have also reported that PPARs can bind to the DR2 PPRE repeats. In PPRESearch the user can search for both DR1 and DR2 type PPRE repeats. This is one of the special features in PPRESearch program where other transcription factor binding programs only predicts DR1 repeats.

       Thus using the above mentioned PPRESearch features provide the good user flexibility which further helps to widen and narrow their search for better prediction of PPRE, making PPRESearch a promising tool for the researches in PPRE prediction.