note remiah <p> Hello ejbiers.<br><br> <code> print "###:".$hit->name . $hit->description."\n"; __DATA__ ###:43989.cce_0262(Cyanothece ATCC 51142) </code> This is first time I looked into BioPerl. I have no idea for why name method stores it, just found it while looking around modules of bio perl.<br><br> Your XML lacks several end tags. <br> And real command line, I guess , <pre> perl scriptname.pl -i inputfile.xml -o goodoutputfile.txt -t test.txt -n 3 -b 1 </pre> I hope you fixing them and get more proper answers from bio perl monks.<br><br> regards. </p> 1006367 1006367