Promoter Motif And Conserved Module Analysis In DNA And RNA Using Almodules

Identification of transcription factor binding sites (TFBSs) elucidates regulation and control of transcription and gene expression. Overprediction of TFBS due to the high abundance of the small binding motifs is a notorious problem. For this comparative evaluation of TFBS is important.The tool AIModules presented in this paper presents an integrated solution for TFBS analysis as Web service and downloadable software. It works for other DNA and RNA motifs as well. Several sequences (DNA and RNA) are searched for TFBSs using predefined matrices from the JASPAR DB or by using own matrices for DNA or RNA motif discovery. Furthermore, AIModules can find TFBS common to two or more sequences. Demanding high or low conservation AIModules outperforms other solutions in speed and finds more modules (specific combinations of TFBS) than alternatives. The web application searches also RNA motifs (e.g. polyadenylation motif) as well as other DNA motifs (e.g. enhancers, silencers) and motif combinations. The application is free and open source to be used on-site or locally. These functionalities allow a number of biological applications, in particular analysis of promoters, including conserved modules and shared TFBSs in conserved gene families, presence of modules, motifs or regulatory elements in mRNA.