I am not very good at computational biology. I am working on a transcriptional repressor protein which is believed to be associated with virulence. I did DNAse 1 footprinting to determine the sequences it binds to a promoter and used the sequence to align promoter sequences from orthologous genes. I then used DMINDA to identify motifs. I want to scan the whole genome for predicting genes that are regulated by this particular transcription factor. Has anyone used DMINDA for whole genome scanning of a  motif? I am not sure if I am doing it right, I uploaded the whole genome sequence in FASTA format, but it shows no hits. I also used DOOR to insert all promoter sequences of the organism and it doesn't work either :( Any suggestions please?  

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