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Recipe: NetSurfP 1.1
Created by LociOiling 1 1
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Name: NetSurfP 1.1
ID: 102282
Created on: Sat, 01/14/2017 - 09:01
Updated on: Sat, 01/14/2017 - 09:01
Description:

Convert NetSurfP webpage output into secondary structure prediction and copy-and-paste spreadsheet format. V1.1 handles blank lines gracefully and adds a confidence prediction.



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LociOiling's picture
User offline. Last seen 46 min 30 sec ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
adds confidence prediction, handles blank lines gracefully

NetSurfP 1.1 reformats the secondary structure prediction from NetSurfP to make it more useful to Foldit players.

NetSurfP 1.1 adds secondary prediction confidence to the output of NetSurfP 1.0. For each segment in the input, the confidence ranges from 0 to 9, with 0 being low confidence. The confidence is simply the first digit of the probability of the winning structure prediction for that segment, so 0.994 gives confidence "9", and 0.590 gives "5".

Sample scriptlog output:

---secondary structure prediction---
LHHHHHHHHHHHHHHLLLLLLLHHHHHHHHHHHHHHLLLLLEEEELLLLEEEEEELLLLLLLLLL
---prediction confidence---
96899999999988758888558899999999987668996688758865678856798666789

NetSurfP 1.1 also ignores blank lines in the input. These blank lines may occur when copying from the NetSurfP output page.

See NetSurfP 1.0 for usage.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Microsoft, Adobe, RosettaCommons