The first is that we simply don't have time to cover everything. The second, and most important reason is that the use of protein sequences for analyses and database queries is always preferred to the use of nucleic acid sequences. This is because there is more information per residue in a protein sequence than in a DNA sequence. For instance, a protein sequence correctly translated from DNA carries with it information about reading frame, start and stop codons and codon redundancy in addition to its 3-dimensional structure and chemical properties. And finally, most analysis programs treat biological sequences as simple strings of text.
Protein sequences, as simple strings of text, are generally more complex and distinguishable.
DNA, on the other hand, in the absence of knowledge about correct reading frames and start and stop locations are far, less rich as simple text strings. We will first take a look at the Dynamic Programming algorithm for sequence comparison that most analysis programs are built upon.