Hi, I want to compare 2 genomic sequences, one is the reference (r) the other is the query, the reference is composed of 2 genes (mitochondria 16kbp each) and the intergenic seq in between, the other is the (q1) sequence which is the left gene in other species (homologous) with the next intergenic sequence in this this species, and another alignment is between the reference (r) and the homologous right gene with the intergenic sequence in this species Note that the 2 genes could be not consecutive in the query specie i.e. if X and Y are two genes and --- is the non coding sequence in between we have X---Y in reference but X---Z---Y in the other species.
I aim at studiying the region between the 2 vertical lines in the picture, what is the best alignment approach to do it ? i.e global/local/semi global/mixte? and what about the alignment parameters i.e match mismatch and gap penalty ?