Python Programming for Biology: Bioinformatics and Beyond

Figure 12.1.  Example alignments of protein and DNA one-letter sequences. Dashes

are used to represent positions where one sequence has a residue with no equivalent in the

other; i.e. a gap is required to pair up the residues properly. Note that with the protein

sequence (left) we can match positions not only by the residues being identical, but also

by the residues being similar.

As  you  might  expect  for  the  cornerstone  technique  of  bioinformatics,  sequence

alignment  comes  in  many  different  varieties.  Which  kind  of  sequence  alignment  is  used

will largely depend upon what kind of biological question is being asked.

1

The following

are examples of situations that sequence alignments may be used for, with attention paid

to what is different about the bioinformatics of each case.