[proteamdavis] Yay! We've got work to do

  • From: Shankar Sankaran <sankar85_s@xxxxxxxxx>
  • To: proteamdavis@xxxxxxxxxxxxx
  • Date: Thu, 8 Jul 2004 18:29:34 -0700 (PDT)

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 
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.

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  • » [proteamdavis] Yay! We've got work to do