Install libsvm-tools using apt or download libsvm-3.24.tar.gz from https://www.csie.ntu.edu.tw/~cjlin/libsvm/ webpage.
Make sure you can use svm-predict in command line.
Predict high reactivity cysteine using model from our paper (doi:10.1021/acs.biochem.7b00897).
Check run_examples.sh in examples/ecoli/ .
If you have your own fasta need to be predict, simply:
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Create a new dir in examples/, enter it
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Collect +/- 20 sequecne of cys
../../scripts/get_align.py [fasta]
- Extract features
../../scripts/get_feature.py
- Predict using our model
svm-predict formated_input ../../models/train_v1.model predict
- Finalize results
../../scripts/get_highact.py