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

Alexander Kozik akozik@2xtreme.net
Wed, 03 Oct 2001 10:01:15 +0000


I enjoy this discussion about orthologues, paralogues and whole genome
There is a program GenomePixelizer for comparative genomics.
It does allow to view gene relationship between genomes based on
sequence identity/similarity:

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