Hello, and thank you for your interest in using our scripts to find amphipathic helices in batch.
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This file is the readme... Read it first!
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This is an executable of the script for Mac OS X 10.6+
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This is an executable of the script for Windows 7 ONLY!!!
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Here is the source code, written in Python3.
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The following scripts were written for the ease of use of extracting the first sequence corresponding to a helix predicted by the Jpred server. They are both source code, so you will need to have python3 installed in order to run them.
When you do a batch job through the Jpred server, they send you an individual email for each input. You will have to extract the body of the emails and concatenate them into one file that serves as the input for the first script, jpred0.2.2.py, which gets rid of all the junk in the email and creates the input for the second script, firsthelix_0.1.py, which extracts the amino acid sequence that corresponds to the first alpha helix sequence that Jpred predicted. The output is a FASTA file that you can use in amphihelix_0.2.2 to get a table with the hydrophobic moments of all the first helices.
When you do a batch job through the Jpred server, they send you an individual email for each input. You will have to extract the body of the emails and concatenate them into one file that serves as the input for the first script, jpred0.2.2.py, which gets rid of all the junk in the email and creates the input for the second script, firsthelix_0.1.py, which extracts the amino acid sequence that corresponds to the first alpha helix sequence that Jpred predicted. The output is a FASTA file that you can use in amphihelix_0.2.2 to get a table with the hydrophobic moments of all the first helices.
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This script extracts only the amino acid sequence and secondary structure predictions from the Jpred output emails.
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This script extracts only the amino acid sequence corresponding to the first helix predicted by Jpred
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