Joining Gaps into Unmatched Regions and Extracting Long Ones from a Sequence Alignment (Step 3 of the Preprocessing Phase)

<p>Gaps <i>ℓ</i><sub>1</sub> and <i>ℓ</i><sub>3</sub> in org1 are joined if the (intragapped) hit <i>ℓ</i><sub>2</sub> is short enough. Assume that <i>ℓ</i><sub>2</sub> and other intra-gapped regions are short enough so that the proximal gaps in org1 are joined to form the unmatched region <i>ℓ</i>. Assume that gaps in org2 are joined similarly to form the unmatched region <i>k,</i> and that the unmatched regions <i>ℓ</i> and <i>k</i> are long enough. If the regions <i>ℓ</i> and <i>k</i> intersect (as in this example), they are joined and the resulting segments in both organisms are extracted to be handled in the next step.</p>