【4.2.1】蛋白质二级结构预测--GOR

一、工具介绍

2.1 在线工具

2.2 本地化程序

2.3 我的案例

GOR IV (c语言的版本) 用法

cd /data/user/sam/project/xten/src/GOR_IV
wget -c http://mig.jouy.inra.fr/sites/all/downloads/Mig/Logiciels/GOR_IV.tar.gz

cd /data/user/sam/project/xten/src/GOR_IV/GOR/SOURCE
make
make install

预测:

cd /data/user/sam/project/xten/src/GOR_IV/GOR

./SOURCE/gorIV -prd test.fa -seq DATABASE/New_KS.267.seq -obs DATABASE/New_KS.267.obs -pro test.out

参数说明:

Usage gorIV -prd Fname1 [-seq Fname2] [-obs Fname3] [-pro Fname4]

Fname1: name of the file containing sequence[s] to be predicted (mandatory)
Fname2: name of the file containing Kabsch-Sander sequence database (DATABASE/New_KS.267.seq)
Fname3: name of the file containing Kabsch-Sander observed secondary structure database (DATABASE/New_KS.267.obs)
Fname4: name of the output file that will contain GOR probabilities

预测的序列不限长度

预测出来的结果,中间都是E这种二级结构

GGGGS   Sequence
CEEEC   Predicted Sec. Struct.

参考资料

  • The GOR Method of Protein Secondary Structure Prediction and Its Application as a Protein Aggregation Prediction Tool
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