Bioperl: Start of alignment debate...

[Lincoln Stein]

Steve Chervitz writes:
 > Ewan,
 > 
 > Regarding this requirement:
 > 
 > 4. The alignment should be able to be changed/manipulated 
 > 
 >   -- Removal/Addition of sequences 
 >   -- Truncated at the N or C terminii 
 >   -- The alignment internally changed 
 > 
 > Not all alignments need to be editable. Removing editability and using
 > factories to create new alignments would simplify the alignment object
 > itself. Having a class of immutable alignments would also ensure that
 > a given alignment hasn't been mangled, when this is important.

I think that the representation of alignments should be designed with
editability in mind.  It might be hard to add editability after the
fact.

Lincoln

 > 
 > Steve Chervitz
 > sac@neomorphic.com
 > 
 > Ewan Birney writes:
 >  > 
 >  > I've started to lay out my ideas about sequence alignments
 >  > for bioperl at
 >  > 
 >  > http://bio.perl.org/Projects/SeqAlign/overview.html
 >  > 
 >  > at this moment it is just trying to gather together a list of
 >  > requirements about alignments. I am sure I have not got them all,
 >  > so if you have some use for alignments, please check the page
 >  > out and tell me what to add.
 >  > 
 >  > 
 >  > Ewan Birney
 >  > <birney@sanger.ac.uk>
 >  > http://www.sanger.ac.uk/Users/birney/
 >  > 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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