I have a number of genes which I'd like to locate in a whole-genome assembly, in order to identify the genes' promoters. In the past I've done this manually using BLAST and BLAT, which has worked well, but the process is quite time-intensive (because I have to take into account introns and exons). Now I find myself in a situation where I need to find the promoters for 100s of genes.
Is there a pipeline or tool which will, given gene sequences and allowing for introns, allow me to identify automate the detection of gene promoters? I'd rather not reinvent the wheel.