Gap Penalty

Until now the central constructs used to measure the value of an alignment have been matches, mismatches and spaces. Now we introduce another important construct, gaps. Gaps help create alignments that better conform to underlying biological models and more closely fit patterns that one expects to find in meaningful alignment. The idea is to take in account the number of continous gaps and not only the number of spaces when calculating an alignment mark This section presents a gap penalty model for evaluating the weight of a sequence of consecutive indel operations. The model states that consecutive indel operations have different total weight than simply the sum of their weights.

 

Example 2.17   Consider the alignment:
S = a t t c - - g a - t g g a c c
T = a - - c g t g a t t - - - c c
which has four gaps containing a total of eight spaces. That alignment would be described as having seven matches, no mismatch, four gaps and eight spaces.