[Bioperl-l] [ANNOUNCE] Sequences with meta data

[Heikki Lehvaslaiho]

Richard,

I committed the Bio::Seq::Meta::Array module. See if it does what you'd
expect it to.

	-Heikki

On Wed, 2003-04-16 at 17:40, Heikki Lehvaslaiho wrote:
> Richard,
> 
> I was away for a week, sorry.
> 
> Bio::Seq::Meta is just one implementation of the interface. It stores
> values in a string and forces the values to be exactly one character
> long. An other implementation might want to store values in an array and
> the length limit goes away. In fact, to provide better base classes, I
> have started writing a class which does that.
> 
> I am calling it Bio::Seq::Meta::Array and I am tempted to rename
> Bio::Seq::Meta into Bio::Seq::Meta::String. More specialised classes
> could then inherit from either depending on their needs. Perl is so much
> more efficient in manipulating strings than arrays that it makes sense
> to use string storage whenever possible.
> 
> I hope to commit the array implementation after Easter.
> 
> 	-Heikki
> 
> 
> On Wed, 2003-04-09 at 12:07, Richard Adams wrote:
> > I've just been looking at the documentation for Bio::Seq::Meta etc.
> >  I can see
> > that where an alternaltive single character alphabet exists and is
> > widely accepted(e.g., chemical properties, 2ndary structure
> > assignation) it should prove very useful. I will try and devise the
> > specs for a  protein secondary structure handling implementation
> > in the next week or so .
> > 
> > But (maybe I'm missing something here) in cases where such an alphabet
> > doesn't exist (e.g., applications predicting regulatory sequences in
> > DNA, where each residue is assigned a probability of existing in a given
> > regulatory region), there is no accepted alphabet - each residue is
> > associated just with a score. A single character representation would be
> > completely arbitrary (e.g A B C D E according to strength of
> > prediction). is
> > this still suitable for Bio::Seq::Meta or is the best way to deal with
> > this sort of data  just to store significant scores
> > as features on the sequence?
> > 
> > Richard
> > 
> > 
> > --
> > Dr Richard Adams
> > Bioinformatician,
> > Psychiatric Genetics Group,
> > Medical Genetics,
> > Molecular Medicine Centre,
> > Western General Hospital,
> > Crewe Rd West,
> > Edinburgh UK
> > EH4 2XU
> > 
> > Tel: 44 131 651 1084
> > richard.adams at ed.ac.uk
> > 
> > 
> > 
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> > Bioperl-l at bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
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