Describe bestfit and gap and explain in which situations you should be using which program. Bestfit is a sequence alignment program which looks for local similarities. It will show multiple areas of the pair of sequences which match quite closely. Its results show only those areas of the two sequences which match quite closely. No gaps are inserted.
Gap is a global sequence alignment program which attempts to align the entire sequence.
After gap is run, it shows both complete sequences and their alignments with gaps inserted to make them approximately the same length. Bestfit should be used where you expect regions within the sequences to be highly conserved, but that other areas should not be aligned together as they are probably not homologous. Modern scoring matrices are based on statistics gathered from a large number of sequence comparisons. Monte Carlo simulation is a method of using random numbers to simulate real-life processes. In sequence alignments, where 2 sequences are being compared, one or both sequences can be randomized and the alignment re-done.