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

[Heikki Lehvaslaiho]

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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-- 
______ _/      _/_____________________________________________________
      _/      _/                      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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