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README
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README
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FR-t5-M : a protein structure prediction program, integrated FR-t5 with MEFTop
Free for academic use only.
For comercial use, please contact Prof. Taijiao Jiang.
All rights reserved.
The FR-t5-M has been tested on Debian and Red Hat Linux (32 bit).
#######################################################
Installation:
(0) Before installation, please make sure the following
softwares or databases are installed properly.
1. Modeller;
2. NR Database (or) u90 Database;
3. FR-t5_data;
4. MEFTop_Model and Fea37_parameter;
5. NNCon
Modeller could be download from the website:
http://salilab.org/modeller/download_installation.html
U90 Database, which is designed by our laboratory, can
be downloaded at:
http://jianglab.ibp.ac.cn/lims/FRt5M/FRt5M.html
FR-t5_data is the structure library for FR-t5 and can be download at:
https://www.synapse.org/#!Synapse:syn10155874
MEFTop_Model and Fea37_parameter are parameter libraries for MEFTop and can be download at:
https://www.synapse.org/#!Synapse:syn10155869
https://www.synapse.org/#!Synapse:syn10155872
NNCon is the contact map predictor and can be download at:
http://sysbio.rnet.missouri.edu/multicom_toolbox/tools.html#license
(1) Uncompress the tar.gz file
tar -zvxf FR-t5-M.tar.gz
(2) Change work path to the package, and open configure.sh
cd FR-t5-M/
cp FR-t5_data/data/* FR-t5-M/FR-t5/data/*
cp MEFTop_Model/Model/* FR-t5-M/MEFTop/Model/*
cp Fea37_parameter/parameter/* FR-t5-M/MEFTop/parameter/*
(3) Set $Modeller_Path to the directory of Modeller;
Set $NR_Database or $U90_Database or both of them;
(4) Save the file.
(5) Run configure.sh to configure it. After that, this
package can be moved to anywhere.
./configure.sh
(6) run assembly.sh to start work, or use the jar file:
java -jar FR-t5-M.jar
#######################################################
How to use:
(1) Run the jar file.
When running the java program, you could submit as much as
5 sequences at a time, which can be loaded from your local
disk or pasted from the clipboard. It's OK to edit the
textbox directly.
To predict protein structures, three directories will be
established in the output path:
1. Input/ Your could find you sequences there.
2. Work/ Main works are done in this directory.
3. Output/ It's the place to store the selected
protein structures.
The standard output and standard error message are redirected
to $ID.stdout and $ID.stderr file, respectively ($ID is your
work ID).
(2) Run the shell script 'assembly.sh'.
For example, if you want to predict the structure of "T0684.fasta",
and it's in "~/Sequence/", you may type the command like that:
./assembly.sh -f ~/Sequence/T0684.fasta -o ~/Result
In this command, "~/Result" is the place for output. If
"-f" option changed to "-d", the scipt will find all the
fasta files in the path specified by the argument after
"-d", and predict their structures:
./assembly.sh -d ~/Sequence/ -o ~/Result
More options can be found if "./assembly.sh" is typed.
(3) UpdateLib.tar.gz could be used to update the library folder FR-t5/data
#######################################################