Hey guys, All right. So we've come up with a plan to make a list of hexamers (6 amino-acid sequences). I've come up with 30 proteins and I am going to split them up among the six of us (I'm leaving Marty out because Paul and I are giving him too much work with the programming already, sorry Marty). So your mission should you choose to accept it, and accept it you will, or else, will be to come up with all (or at least 10) possible pentamers (5 sequence amino acids) and all (or at least 10) possible hexamers for the protein IDs assigned to you. So you have to open up each protein file (Go to www.pdb.org and type in the given ID. Then click on Sequence Details and scroll down to sequence and secondary structure.) Now you want to note down all the possible pentamer and hexamer sequences (they are all in one letter codes) with 'H' under them (H is for helix). But wait there's more.... Now for every sequence you find you need to type it up in the following format and save it in a text file: searcher.sh onelettersequence.txt threeletter sequence for example lets say one of my sequences is VPLLIM, the line I would type would be: searcher.sh vpllim.txt Val Pro Leu Leu Ile Met So do that for all your sequences and save it in a text file. If you need to know what the one letter sequences corresponding three letter sequences are, consult one of the bio books. then email me your text file full of sequences in the above format and i will type them in and get the searches started. If any of that did not make sense email me or come and talk to me. So here is the list: Paul: 12AS, 1A35, 1A48, 1A8H, 1ADJ Tejal: 1ASY, 1ATI, 1B04, 1B70, 1B76 Nancy: 1B7Y, 1B8A, 1BBU, 1BD0, 1BNC Neela: 1BS1, 1CG4, 1DRG, 1DTS, 1DV1 Josh: 1A59, 1AAT, 1ACA, 1AL8, 1BUC Me: 1AIQ, 1C1K, 1C2P, 1BIS, 1BPZ I am not sure if the 'o's should be zeroes or the zeroes should be o's so if one doesn't work try the others. All righty then, knock yourselves out. Shankar --------------------------------- Do you Yahoo!? Yahoo! Mail - You care about security. So do we.