Assigning Gap Penalty Values
Gap penalty values are designed to reduce the score when an alignment has been disturbed by indels. The value should be small enough to allow a previously accumulated alignment to continue with an insertion in one of the sequences but should not be so large that this previous alignment score is removed completely. There are two strategies when assigning values to gaps:
- Keep the score similar regardless of gap length. Allow a constant overall gap penalty regardless of gap length. Thereofre assign no gap extension penalty and only penalize the sequence when there is a gap open. This will penalize a large gap by the same extent as a small gap.
- Make the score becomes larger as a linear function of gap length. Have a larger gap opening penalty followed by a gap extension penalty that is smaller than the gap open penalty. This will penalize several small gaps by the same extent as 1 large gap.
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