I plan to compare the promoter region of same genes in pan-genome (a set of genomes of different strains of a species).
I have sequencing data of the genomes I need. Some are fully annotated and some are not. I arbitrarily define the promoter region as 1.5kb upstream of the start codon (even though this is not an exact definition of a promoter). I plan to extract the "promoter" sequence of each gene, and do multiple alignments of them to explore if there is any conserved pattern or special feature.
I am new to pan-genome research. Could you recommend any tool or program to realize my plan?
Also, how the program you recommend recognize and extract promoter regions of the same gene across the pan-genome (not its duplicates or paralogs)?
Thanks for your help.