[Bioperl-l] non-palindromic issue in Bio::Restriction::Analysis
apurva at cshl.edu
Wed Jun 6 23:51:45 UTC 2007
I was hoping you could confirm and give me some feedback on an issue
I think I've found with the Bio::Restriction::Analysis module. I am
using the enzyme AciI, a non-palindromic restriction enzyme with a 5'
C | CGC 3' recognition site. The module should search both the
forward and the reverse complement strings in the case of a non-
palindromic enzyme. I have found that the this works only
intermittently. For example, the following sequence:
Should digest into 10 fragments using this enzyme, but the module
produces only 7. Could you please confirm this behavior, and if
observed, suggest some possible fixes? This may be a bug in the
_non_pal_enz method, or may be me overlooking something pretty obvious.
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