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README
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===========
WARNING!!!!
===========
This package is out-of-date. It has been splitted into two packages:
1) TGT_Package
https://github.com/realbigws/TGT_Package
2) Predict_Property
https://github.com/realbigws/Predict_Property
The TGT_Package is used for generating the TGT file from a given sequence in FASTA format.
The Predict_Property is used for predicting protein local properties from a given TGT file or FASTA file.
Thus, the RaptorX_Property_Fast module won't be updated anymore.
===================================
RaptorX Property Standalone Package
(v1.02) 2018.05.18
===================================
Title:
RaptorX-Property: a Standalone Package for Protein Structure Property Prediction
Author:
Sheng Wang
Email:
realbigws@gmail.com
============
Publication:
============
[1]
RaptorX-Property: a Web Server for Protein Structure Property Prediction
Sheng Wang#*, Wei Li*, Shiwang Liu, Jinbo Xu#
Nucleic Acids Research, 2016
[2]
Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields
Sheng Wang#, Jian Peng, Jianzhu Ma, Jinbo Xu#
Scientific Reports, 2016
[3]
AUCpreD: Proteome-level Protein Disorder Prediction by AUC-maximized Deep Convolutional Neural Fields
Sheng Wang#, Jianzhu Ma, Jinbo Xu#
ECCB, 2016
Bioinformatics, 2016
[4]
AUC-maximized Deep Convolutional Neural Fields for Protein Sequence Labeling
Sheng Wang, Siqi Sun, Jinbo Xu#
ECML/PKDD, 2016
========
Install:
========
1. download the package
git clone https://github.com/realbigws/RaptorX_Property_Fast
cd RaptorX_Property_Fast
--------------
2. compile
cd source_code/
make
cd ../
--------------
3. setup
./setup.pl
[note]:
before you run anything, type the above command for configuration just for once.
=========
Database:
=========
1. if databases/uniprot20 not exist, create it by
mkdir -p databases/uniprot20
2. download the UniProt20 database from the following link:
http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/uniprot20_2016_02.tgz
uncompressed it, and move all files or symbol link to databases/uniprot20_2016_02
3. if other version of UniProt20 is applied, then use '-d uniprot20_XXXX' option in ./Fast_TGT.sh
4. note that the new UniClust30 database could also be applied, such as:
http://wwwuser.gwdg.de/~compbiol/uniclust/2017_10/uniclust30_2017_10_hhsuite.tar.gz
=======
Server:
=======
1. Please try to use our RaptorX Property server at:
http://raptorx.uchicago.edu/StructurePropertyPred/predict/
2. Users may also use the 'curl' command to submit their jobs. For example,
curl --form jobname=test_job --form email=user@domain --form sequences=ENIEVHMLNKGAEGAMVFEPAYIKANPGDTVTFIPVDKGHNVESIKDMIPEGAEKFKSKINENYVLTVTQPGAYLVKCTPHYAMGMIALIAVGDSPANLDQIVSAKKPKIVQERLEKVIASAK http://raptorx.uchicago.edu/StructurePropertyPred/curl/
[note]:
(i) the 'email' is NOT required.
(ii) the 'job_url' and 'down_url' will be displayed after the 'curl' command is executed.
3. I have also implemented a simplified and command-line version of 'curl'. See below,
https://github.com/realbigws/curl_command
======
Usage:
======
./oneline_command.sh <input_fasta> <out_dir> [cpu_number] [PROF_or_NOT]
-------
Here the first input argument is the input sequence in FASTA format,
the second input is the CPU number,
the third input is to use profile or not.
-------
./PDBTM_Topology_Pred.sh -i example/1bhaA.tgt -l example/1bhaA.pdbtm
The module to predict transmembrane topology.
================
Running example:
================
1. use sequence profile:
cp example/T0530.fasta .
cp example/T0530.tgt .
./oneline_command.sh T0530.fasta tmp 1 1
or,
./oneline_command.sh example/T0530.fasta tmp 1 1
-----------------------
2. not use sequence profile:
./oneline_command.sh example/T0530.fasta tmp 1 0
-----------------------
The output files should be found in the tmp/T0530/ folder
=============
Output files:
=============
1. overall detailed results:
SeqID.all
e.g., file 'T0530.all' in tmp/T0530/ folder. This file contains all the detail prediction results for Secondary Structure Element (SS3 and SS8), Solvent Accessbility (ACC), and Order/Disorder prediction (DISO)
------------------
2. detailed results in separate files:
SeqID.ss3
SeqID.ss8
SeqID.acc
SeqID.diso
These files contain the detail prediction results in the form of probability.
------------------
3. simple results in separate files:
SeqID.ss3_simp
SeqID.ss8_simp
SeqID.acc_simp
SeqID.diso_simp
These files contain the simple predicion results in onee line.
------------------