I and others would be very interested in seeing some of these errors, I'm sure, but right off the top of my head, you might try the following changes:

my $genfile = 'c:\bemisia_coi.gb';

and

 my @line = split(/\/\//,$line); # If you want to split on //

and

my $sequence = "/origin(\*+)\/\/\"; # as above

Good on you for using strict and warnings, though. The specific errors that you're getting will do wonders for helping us understand what specific problems you have.

In reply to Re: Spltting Genbank File by starX
in thread Spltting Genbank File by perl_n00b

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