[Bioperl-l] Bio::Variation committed [Project: Computational Mutation Expression Toolkit]

[Heikki Lehvaslaiho]

Hi,

I just committed Bio::Variation files to bioperl-live. All in all 10
classes and 185 tests in seven t files. 'cvs update -d' and you can
see them all. Easiest way of getting grips with what these classes can
do is to have a look at test input files, e.g. t/mutation.dat.

You'll need Bio::LiveSeq to actually generate the information from
sequnces, but those files are not committed, yet.

	-Heikki


Heikki Lehvaslaiho wrote:
> 
> Dear Bioperlers,
> 
> We'd like to announce a project to add classes into Bioperl to handle
> sequence variations.
> 
> The Computational Mutation Expression Toolkit project consists of two
> sets of Bioperl classes:
> 
> Bio::LiveSeq
> 
> Bio::LiveSeq name space contains a set of modules to read in (EMBL
> formatted) sequences and create a data structure (double linked list)
> to represent the DNA sequence. A model of an eucaryotic gene is built
> by creating virtual exon, transcript and translation objects which are
> dependant on the DNA sequence object. This novel strategy allows us to
> handle biological sequences in a way that makes it extremely easy to
> deal with sequence variations and coordinate system changes. The
> results can be written out as Bio::Variation objects.
> 
> Bio::Variation
> 
> Bio::Variation name space contains modules to store sequence variation
> information as differences between the reference sequence and changed
> sequences. Also included are classes to write out and recrete objects
> from EMBL-like flat files and XML. Lastly, there are simple classes to
> create some sequence change objects. At the moment, we do not have
> methods to create bioperl sequence objects from diffs but they should
> be easy to add.
> 
> We've set up web pages with more information about the project:
> 
>         http://www.ebi.ac.uk/mutations/toolkit/
> 
> We'll start committing code to CVS shortly (or after summer holidays).
> 
>     Heikki Lehvaslaiho & Joseph Insana
>      heikki@ebi.ac.uk    insana@ebi.ac.uk
> 
> --
> ______ _/      _/_____________________________________________________
>       _/      _/                      http://www.ebi.ac.uk/mutations/
>      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
>      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
> ___ _/_/_/_/_/________________________________________________________
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________