[Bioperl-l] RE: Comparative genomics - regions of synteny and whole genome duplication

[Alexander Kozik]

Hi,

I enjoy this discussion about orthologues, paralogues and whole genome
duplications.
There is a program GenomePixelizer for comparative genomics.
http://www.atgc.org/GenomePixelizer/GenomePixelizer_Welcome.html
It does allow to view gene relationship between genomes based on
sequence identity/similarity:
http://www.atgc.org/GenomePixelizer/Examples/GenoPix_Example_arab-worm-inter.html

This type of visualization may help to think about the origin of gene
duplication events.
It is written in Tcl/Tk. However it may be re-written in Perl/Tk.
The weak side of GenomePixelizer is an absence of automatic pipeline
(scripts) that
generates distance matrix file from Blast, Fasta or ClustalW output.
This is the place where BioPerl could really help.
Sorry if this message is out of topic.

Alexander Kozik
Department of Vegetable Crops
Asmundson Hall
University California at Davis
tel: (530) 752-1742
email: akozik@atgc.org
http://www.atgc.org