TALgetter allows you to scan input sequences for putative target sites of a given TAL (transcription activator like) effector as typically expressed by many Xanthomonas bacteria. TALgetter uses a local mixture model, which assumes that the nucleotide at each position of a putative target site may either be determined by the binding specificity of the RVD at that position (if binding occurs at that position) or by the genomic context (if no binding occurs). Binding specificities and importance of the individual RVDs has been trained on known TAL effector - target site pairs. Nucleotide preferences of the genomic context are learned from (putative) promoter sequences of A. thaliana and O. sativa.
TALgetter is available as a web-application at . Here, you can also download a command line application that is easily scriptable.
TALgetter is implemented in Java using Jstacs. Here, can download the Jar of the command line application. In addition, we provide the Jar of the Galaxy web-application for installing it in your local Galaxy server.