FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting

Abstract

FOOTER is a newly developed algorithm that analyzes homologous mammalian promoter sequences in order to identify transcriptional DNA regulatory 'signals'. FOOTER uses prior knowledge about the binding site preferences of the transcription factors (TFs) in the form of position-specific scoring matrices (PSSMs). The PSSM models are generated from known mammalian binding sites from the TRANSFAC database. In a test set of 72 confirmed binding sites (most of them not present in TRANSFAC) of 19 TFs, it exhibited 83% sensitivity and 72% specificity. FOOTER is accessible over the web at http://biodev.hgen.pitt.edu/Footer/.

Figure 1

Flowchart of the execution of web-tool FOOTER. Protein or DNA sequences can be entered in the input. In the first case, a series of BLAST (15) searches will be performed to identify the homologous promoter sequences. The DNA sequences will be aligned and putative motifs will be compared pairwise as we describe in the text.

Figure 2

Example of FOOTER output. The predicted sites are presented in table format and in the PNG formatted figure. The figure displays the alignment of the two promoter sequences, colour-coded by conservation percentage.