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We only insert those gaps of t_{k} into the MSA that are not
already present in a_{k}. Also, when a gap in t_{k} overlaps
with a gap in a_{k}, we only insert the the part of the gap that
is not already present in a_{k} (see Figure 9,
large X).
Since each gap of t_{k} that is considered is inserted into
all sequences
,
the partial score
is still optimal: gap against gap scores zero. In
Figure 9, the up arrow correspond to this step. In
the example one gap is inserted into the MSA (tall dark
rectangle). The large "X" marks the gap that is already present
and is therefore not inserted.
Figure 9:
Steps 2 and 3: all gaps from t_{k} are
inserted into the MSA, and all gaps from a_{k} are inserted into
t_{k} and t_{k+1}

Chantal Korostensky
19990714