Motif search strategy. A) Diagram of the bioinformatic workflow for sequence analysis. A subgroup of sequences from the one-hybrid assay was used to search for motifs using MEME. Logos on the right represent the position-dependent matrix based in the alignment for GLI transcription factor candidate motifs. The matrix was also used as input to the MAST algorithm to identify potential Gli-binding sites in non-coding regions of candidate genes. B) Motifs identified with MEME/MAST strategy. Logos represent the alignment of the potential binding sites identified in each sequence in both upstream (left column) and intronic (right column) for nine candidate genes. Numbers of potential binding sites are indicated in brackets next to gene name. C) Gene ontology table for selected putative target genes found in (B).
Milla et al. BMC Genomics 2012 13:2 doi:10.1186/1471-2164-13-2