Thanks a lot for your reply, LanX. That makes sense :)

Will have a look at the code to see what is wrong

In particular, consider the statement
    my $alphabet = qw( A T G C );
and maybe do a little experiment to print  $alphabet and see just what it is.

Update: The next statement
    my @bases = @$alphabet;
suggests  $alphabet is supposed to be an array reference that is de-referenced to initialize the  @bases array, but since  $alphabet is used nowhere else, why not just initialize  @bases directly from the  qw(A T G C) list of bases?

You're absolutely right. I copied-pasted the code from bioperl.org onto this post without checking to see if it was wrong. When I used it in my terminal, I typed it all out and automatically changed the $ sign in $alphabet to an @, which is why it worked fine for me. And I agree, I should have gone for @bases directly instead of using that extra array which is not used anywhere else in the code. I will pay more attention to these details next time I code something up, so thanks for the tip!

On another note, I'd like to go back to my original question. I now understand that this foreach loop is being used to repeat its code (k-1) times. Let's assume $k = 3.

When $_ = 1 (first iteration of the foreach loop), we make the strings (AA, AT, AG... CC) and push them all into @newwords.

When $_ = 2, if we repeated the code inside the loop, we should produce another set of (AA...CC) and push them into @newwords, which is reinitialised in this second iteration through the loop.

I know this is not the case, however, because if I add the following code:

print "@newwords\n"


after this line:

push (@newwords, $w.$b);

we can see that we are now pushing (AAA...CCC) to the @newwords array, despite the code being exactly the same as in the first iteration.
This is exactly what I want my code to do, although I don't understand why it is working. We are pushing 3-character strings, although according to this code, we are only pushing strings of two characters ($w.$b) into the @newwords array.