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Split and shifted gaps

In many MSAs both situations will arise: gaps are shifted and split.
Example 2.2:  In the MSA of Figure [*], sequence A has two gaps and sequence B has three gaps. If we push the gaps together and move them to the same position, we combine 5 events to one single event. In addition, the resulting alignment has a better score (the optimal score in this case) and also makes more sense from a biological point of view.
  
Figure: Here 5 events can be reduced to one event by shifting and fusing the gaps.



Score:   104.635     Score:   240.139
Maximum: 240.139     Maximum: 240.139

                         Event 1
A: RPC__VCP_VLRQ     A: RPCVCP___VLRQ
B: RPC_A_CPV_LRQ     B: RPCACP___VLRQ
C: KPCVCPRQLVLRQ  => C: KPCVCPRQLVLRQ
D: KPCVCPRQLVLRQ     D: KPCVCPRQLVLRQ
E: KPCLCPKQAAVKQ     E: KPCLCPKQAAVKQ



\psfig{file=gaps/splitshiftedgaps.eps,height=0.12\textheight,angle=0}



Chantal Korostensky
1999-07-14