Gap Penalty

Up until now the central elements used to measure the score of an alignment have been matches, mismatches and spaces. Now we introduce another important element, gaps. Gaps help create alignments that better conform to underlying biological models and more closely fit patterns that one expects to find in meaningful alignments. The idea is to take in account the number of contiguous 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.  
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