I'm new to bioinformatics and I have a question. I have a known transcription factor binding site, it has a consensus sequence which varies slightly between different species of fungi, but the core 5 nucleotides remain the same. I have tried scanning genomes for this sequence, but its short nature causes too many unspecific hits.
I need to find this sequence in a number of genes that I believe are regulated by it. What is the best way of doing this? I have limited knowledge of python.