Insertions and Deletions

- 1.
- Point accepted mutations. Base
*i*mutates to base*j*. - 2.
- Insertions. A subsequence of DNA is inserted into a sequence.
- 3.
- Deletions. A subsequence of DNA is deleted from a sequence.

In the simplest theoretical model, all
sequence mutations are explained as deletions and insertions of
genetic material. A point accepted mutation corresponds to a deletion
of a base followed by the insertion of a base at the same position in
the sequence. Gene shuffling can be
viewed as a series of deletion and insertion sequences. However, such
a simplistic model does not take into account the relative
probabilities of such events occuring. Intuitively, the probability of
a single point mutation seems as though it would be much higher than
the probability of an deletion event followed by an insertion event at
the same position in the sequence.
For this reason, we distinguish
between point mutations and insertion/deletion events (*indels*).

As is the case with our model for point mutations, our model for deletions and
insertions is entirely symmetric. Given an alignment of two sequences
*A*, *B*containing at least one insertion or deletion event such as the
following:

Sequence A: ALAEGLGVIACIGEKLDEREAGITEKVVFEQTKVIADNVKDW Sequence B: CKNLGLETIVCTNN______________INTSKAVAALSPDYwe can not determine whether sequence