[Bioperl-l] Bio::Variation committed [Project: Computational Mutation Expression
Wed, 19 Jul 2000 14:35:46 +0100
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 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 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
> firstname.lastname@example.org email@example.com
> ______ _/ _/_____________________________________________________
> _/ _/ http://www.ebi.ac.uk/mutations/
> _/ _/ _/ Heikki Lehvaslaiho firstname.lastname@example.org
> _/_/_/_/_/ 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
______ _/ _/_____________________________________________________
_/ _/ http://www.ebi.ac.uk/mutations/
_/ _/ _/ Heikki Lehvaslaiho email@example.com
_/_/_/_/_/ 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