Transcription factor binding sites detection by using alignment-based approach.

Gene expression is the main cause for the existence of various phenotypes. Through this procedure, the information stored in DNA rises to the phenotype. Essentially, gene expression is dependent upon the successful binding of transcription factors (TFs) - a specific type of proteins - to explicit positions in its upstream, TF binding sites (TFBSs). Unfortunately, finding these TFBSs is costly and laborious; therefore, discovering TFBSs computationally is a significant problem that many researches endeavor to solve. In this paper, a new TFBS discovery method is presented by considering known biological facts about TFBSs. The input to this method includes sequences with arbitrary lengths and the output comprises positions that tend to be TFBS. Through the application of previous methods along with a method that focuses on biological and simulated datasets, it is shown that this method achieves higher accuracy in discovering TFBSs.