Bioperl-guts: Reimplementation etc.

[Kate]

> Hmm. Why deleting ? This would cause a problem with Blast searches
> numbering scheme (it would be difficult to trace back the original
> sequence coordinates from the match if there is a deletion).
> Masking is a very important issue, however; maybe a Bio::Mask could suit
> ?
>
  I'm a software test engineer, so I'm not aware of all the needs of the
biotech community.  If masking works better, its fine by me.:)

                                                           Kate

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