Bioperl-guts: Reimplementation etc.

Matthew Pocock mrp@sanger.ac.uk
Tue, 24 Aug 1999 09:34:30 +0100


I think there will be a general need for a SequenceView object that
concatenates an ordered list of ranges within another sequence. This would be
usefull for representing some ungapped alignments. It would let you do things
like have an alignment of a PDB sequence with a secondary structure with an
embl file, and suck out the regions of the alignment that have info from all
three sources. Loads of other usefull things could be done this way.

Kate wrote:

> > 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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