Here's your problem:

    foreach $motiffile(@motiffile){
        if($motiffile =~ /(^[A|S]\d+\s+|^[A|S]\d+b\s+)([A-Z]+)(\s+.*)$
+/){
        my $name = $1;
        my $site = $2;
        $regexp = IUB_to_regexp($site);
        $motif_hash{$name} = "$site $regexp\n";
        print "motif : $site\n";
        print "The regexp : $regexp\n";
        }     
           }    
           return $regexp;
         ...
[download]

You start to loop through the array @motiffile, but as you get through to the end of this snippet, you return from the sub with one result, thus leaving the loop.

What you can do is collect all results, for example by using this instead of the return statement:

push @regexp, $regexp
[download]

(and of course, @regexp must be declared higher up in the sub), and after the loop block, return a combined regexp:

return join '|', @regexp;
[download]

update Oops, I misread the code (bad indentation), you return after the loop block, instead of in it... But the end result is nearly the same, except now you return the last $regexp instead of the first.

Put my push statement in the loop block.

---

---

Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!

Titles consisting of a single word are discouraged, and in most cases are disallowed outright.

Read Where should I post X? if you're not absolutely sure you're posting in the right place.

Please read these before you post! —

• How do I compose an effective node title?
• How do I post a question effectively?
• Markup in the Monastery

Posts may use any of the Perl Monks Approved HTML tags:

a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr

You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)

	For:		Use:
	&		&
	<		&lt;
	>		&gt;
	[		&#91;
	]		&#93;

Link using PerlMonks shortcuts! What shortcuts can I use for linking?

See Writeup Formatting Tips and other pages linked from there for more info.