[Bioperl-l] Changes to Bio::Tools::SiRNA

[Donald Jackson]

Hi,

I've made (and committed) some pretty major changes to Bio::Tools::SiRNA 
to allow it to accomodate alternative rules for designing siRNA 
reagents.  The actual siRNA selection is now handled by 
Bio::Tools::SiRNA::Ruleset objects.  I also committed two Rulets. 
Bio::Tools::SiRNA::Ruleset::tuschl, which implements the Tuschl group's 
rules that used to be in Bio::Tools::SiRNA, and 
Bio::Tools::SiRNA::Ruleset::saigo, which implements the rules published 
by Ui-Tei et al (2004) (I stuck with the convention of naming the rules 
after the corresponding author).   The Tuschl rules are used by default.

I hope that these changes will make it easier to add more rule sets  
while maintaining backwards compatibility.  As always, I welcome feeback 
on bugs, coding style, or other issues.

Thanks,

Don Jackson
BMS Bioinformatics