Hi, your code looks like you're not using use strict in your script. I, personally, would be afraid to let anyone play around with gene information without being strict.

update:
other Tips:

* use shift for getting the subroutine's arguments.

* splice(@array, 0, 2) should do the same like shifting the array two times.

* use an array for what you want to return; push new elements to it; return the joined array.

sub parseGeneEntry { 
    my $genesList = shift;
    my @genes  = split /\t/, $genesList;

    # should be identical with shifting @genes two times;
    splice( @genes, 0, 2 );

    my @return;
    foreach my $element ( @genes ){
        push @return, $element;
    }

    return join "\t", @return;
}
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PS: untested

edit: changed doc links; added 'my' to $genesList;

edit2:
OMG, it can be further shortened (in case you don't want to do anything further in that sub:

sub parseGeneEntry { 
    my $genesList = shift;
    my @genes  = split /\t/, $genesList;

    # should be identical with shifting @genes two times;
    splice( @genes, 0, 2 );

    return join "\t", @genes;
}
[download]