trouble interpretating phage display peptide screens

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trouble interpretating phage display peptide screens

Postby Siltsje » Apr 14 2015 7:29 am

hi, I have some trouble with the output of my selection experiments using a phage display peptide screen (7 mer). I used NGS sequencing after round one and two of selection and now have 3.4 million seqeunces. I did some quality control and some one recommended to check sequences with the sarotup data base. Still I have more than a million sequences left? Is there anyone who nows what I can do next? many thanks in advance.
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Re: trouble interpretating phage display peptide screens

Postby mchlbrmn » Apr 18 2015 1:18 am

if you don't mind some uninformed thought... How about simply comparing sequence frequency before and after the selections and rank the ones most enriched? (If there are enough copies of each to start with?) But, perhaps the Sarotup is more sophisticated?
If you've done enough rounds of selection, and you really have millions of clones without some really standing out, perhaps the selection method was not stringent or specific enough?
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Re: trouble interpretating phage display peptide screens

Postby Siltsje » Apr 19 2015 2:21 am

Hi. Thank you for your reply. Of course I looked at the frequency distribution. However the top peptides are defined as a " tup" is sarotup database. Removing these I still see based on frequency interesting candidates but aren't there more trics to in a more defined way determin specific candidate peptides? I can just let synthesize a few from the top and see what happens... However doing it this way is quite costly and laborious. I cannot to this in a high throughput way...
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