[Bioperl-l] Project: Computational Mutation Expression Toolkit

Heikki Lehvaslaiho heikki@ebi.ac.uk
Fri, 14 Jul 2000 12:59:21 +0100

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 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 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:


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
___ _/_/_/_/_/________________________________________________________