Sean, I'm writing some PHP-Perl interface code and I can't seem to make this Perl script (ps_scan.pl) run on a web server (other than my own local copy). See attached file (or if it's not here, it's probably in your private email box). It's a binary for a Linux/Intel box. Binaries for other platforms are at the PROSITE site: ftp://us.expasy.org/databases/prosite/tools/ps_scan/ Would it be possible for you to upload it to some HTDOCS (web document root) folder at bioinformatics.org? Plus these two files: php_perl.php <?php print "<H2>Test PHP script that runs a Perl scrip</H2>"; $output = `perl ps_scan.pl seq.dat` print $output; ?> probe.dat >gi|24653663|ref|NM_079018.2| Unknown CG10119-PA (LamC), prot MFNFVLLAILCKIVCLGLKLILLTLRHPSINLSVSNLVKHFQF Or, if it's too much of a bother to you, could you give me write access to the biophp project's HTDOCS folder? Thanks! Also, I've finally thought of an immediate use for your eFetch/ eUtils set of modules. I'd like to submit a protein sequence (like the one shown above) to NCBI'S BLAST server and get some matches, from within a PHP script. Could you provide some info on how your code can be used for this purpose (or how it can be extended/modified to do this)? Or better yet, maybe you could do the necessary coding (when your BRAIN STOPS HURTING, that is). I've finally read your code (parse, parse_fasta, seqfactory, etc), and will be giving more specific comments/questions soon. Thanks! Regards, Serge Need a new email address that people can remember Check out the new EudoraMail at http://www.eudoramail.com