[Bioperl-l] Please help me with the parameters for precise alignment

[ze cheng]

Hello,
      I have been using a alignment tool called NAP
which aligns DNA with protein. It is usually OK until
the alignment problems are very close to each other.
For inst, if I have some insertions at position 6 and
some deletions at position 12, what happened is the
sequence in between that should be correctly aligned
to 6-12 will be shifted forward. (not because the
insertion) The counter part of these bases in the wt
strand is not matched with the part in the input
sequence any more. The mismatch I have used is
BLOSUM62, gap open =10, gap ext =2/5 (I have tried 2
and 5 but neither works out). Thank you for any hint
or suggestion. Have a good one.
      ginger

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