You have two genetically identical samples of E. coli. You expose one sample to radiation, and then culture the bacteria in colder-than-ideal conditions. After several generations, you isolate a strain from the “cold” sample that grows better at cold temperatures than the original “wildtype” sample. You hypothesize that this new strain is no longer genetically identical to the wildtype strain, and that changes in the genome have improved its ability to grow in cold conditions. A previous study has suggested that a protein called SWTR is somehow involved in the adaptation to cold environments. Therefore, your first step in investigating your hypothesis is to sequence the swtr gene from both the cold and wildtype strains.
You use pairwise sequence alignment to compare the sequences.