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Database scanning

The techniques described in the previous sections all assume that we already have two or more sequences to align. However, if we have just determined a new sequence, then our first task is to find out whether it shares similarities with other proteins that have already been sequenced. To do this we must compare our sequence to the sequence database(s) using some computer algorithm. Any of the methods described in the previous sections may be used, but database scanning presents special problems that have led to the development of specialist algorithms. In this section I will review the options and goals of these methods.