Usually, the Spliced Alignment assumes that genomic sequence (the one you want discover its exon-intron structure) and target sequence (a real sequence from a database) are written in the same alphabet. Example: your genomic sequence is a DNA sequence and your target sequence is a cDNA. But I saw an exercise in which you have to modify the recurrence relations to handle the case when genomic sequence and target sequence are written in different alphabets. (Example: genomic sequence is a DNA sequence and target sequence is a protein sequence). I would like to know if just translating the protein sequence to DNA sequence, would be simpler (and maybe more efficient) than changing the recurrence relations of the spliced algorithm to solve the different alphabets case?
