hey guys, okay so there is one more change I want to make in the syntax, right now we type it up as: searcher.sh onelettersequence.txt onelettersequence for example: searcher.sh llaavv.txt llaavv it would be better if you can write the syntax as: searcher.sh resultsPROTEINI.D./onelettersequence.txt oneletter sequence for example: searcher.sh results1AIQ/llaavv.txt llaavv Where "ProteinID" is which protein you got the sequence from (if you are writing all the sequences from one protein into one text file, then the protein id throughout the entire text file would be the same). If this doesnt make sense, talk to me. Shankar __________________________________ Do you Yahoo!? Yahoo! Mail is new and improved - Check it out! http://promotions.yahoo.com/new_mail