sally123,

Two things immediately jump out!


Untested, this should get you started. 
#!/usr/bin/perl -w

use strict;

open my $FH, "<", "./sample.txt";

my %count = ();

while ( my $genome = <$FH> )
{   ....

}

[download]

A good practice is to define the scope of your variables (my, local, our).

Good Luck

"Well done is better than well said." - Benjamin Franklin

In reply to Re: Counting overlapping dimers for multiple sequences by flexvault
in thread Counting overlapping dimers for multiple sequences by sally123

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