[BioRuby] help to understand the codes
chen_li3 at yahoo.com
Fri Jun 19 15:21:27 UTC 2009
Thank you for the info.
Now I think I understand much better about the codes: What the script does is to search a stretch nts of 23 bp and check if it fits the rules: the first two nts and the last two nts are actually the overhanged nts and
the middle part is the core of the sirna.
One more question:
When I read method # uitei?(target) I see an instant variable called @target_size but it is defined in another method # design(rule='uitei').
Since Ruby reads codes from top to bottom, isn't' it better to define #design(rule='uitei') first then followed by # uitei?(target)? Or it is just personal preference?
# Ui-Tei's rule.
start_pos = @target_size - one_third - 1
# rule can be one of 'uitei' (default) and 'reynolds'.
def design(rule = 'uitei')
@target_size = @antisense_size + 2
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