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README
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===================================
Predict_Property standalone package
(v1.01) 2018.10.01
===================================
Title:
Predict_Property: a Standalone Package for Protein Structure Property Prediction
Abstract:
This package predicts Secondary Structure Element (SS3 and SS8), Solvent Accessibility (ACC), Order/Disorder prediction (DISO), and TransMembrane topology (TM2 and TM8) for the input protein using either pure sequence information or evolutionary profile information.
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
[5]
PredMP: a web server for de novo prediction and visualization of membrane proteins
Sheng Wang#, Shiyang Fei, Zongan Wang, Yu Li, Jinbo Xu, Feng Zhao#, Xin Gao#
Bioinformatics, 2018
========
Install:
========
1. download the package
git clone https://github.com/realbigws/Predict_Property
--------------
2. compile
cd source_code/
make
cd ../
--------------
3. the package to generate evolutionary profile information in TGT format could be found at:
https://github.com/realbigws/TGT_Package
======
Usage:
======
#----------- Predict_Property --------------#
Predict_Property v1.02 [Mar-05-2019]
Predict protein local properties using sequence or profile information
USAGE: ./Predict_Property.sh <-i input_fasta | input_tgt> [-o out_root]
[-t diso_thres] [-T topo_thres] [-H home]
Options:
***** required arguments *****
-i input_fasta : input protein sequence file in FASTA format
(or)
-i input_tgt : input protein profile file in TGT format
***** optional arguments *****
-o out_root : default output would the current directory.
[default = './${input_name}_PROP']
-t diso_thres : threshold to determine disordered residue. [default = 0.5]
-T topo_thres : threshold to determine transmembrane residue. [default = 0.5]
-H home : home directory of Predict_Property.sh
[default = ~/GitBucket/Predict_Property]
#------------ AUCpreD -----------------------#
AUCpreD v1.04 [Oct-01-2018]
Predict order/disorder regions using sequence or profile information
USAGE: ./AUCpreD.sh <-i input_fasta | input_tgt> [-o out_root]
[-t threshold] [-k keep_file] [-l real_label] [-H home]
Options:
***** required arguments *****
-i input_fasta : input protein sequence file in FASTA format
(or)
-i input_tgt : input protein profile file in TGT format
***** optional arguments *****
-o out_root : default output would be XXXX.diso_MODE at the current directory,
where XXXX is the input name, and MODE is profile or noprof.
[default = './' ]
-t threshold : threshold to determine disordered residue. [default = 0.5]
-k keep_file : keep the intermediate files if its value is 1 [default = 0]
-l real_label : real Order/Disorder label file, in three lines [default = null]
-H home : home directory of AUCpreD.sh
[default = ~/GitBucket/Predict_Property]
#------------ PDBTM_Topology_Pred ------------#
PDBTM_Topology_Pred v1.05 [Mar-05-2019]
Predict PDBTM Topology labels using sequence or profile information
USAGE: ./PDBTM_Topology_Pred.sh <-i input_fasta | input_tgt> [-o out_root]
[-t threshold] [-k keep_file] [-l real_label] [-H home]
Options:
***** required arguments *****
-i input_fasta : input protein sequence file in FASTA format
(or)
-i input_tgt : input protein profile file in TGT format
***** optional arguments *****
-o out_root : default output would be XXXX.topo_MODE at the current directory,
where XXXX is the input name, and MODE is profile or noprof.
we also output XXXX.topo_simp for simplified result.
[default = './' ]
-t threshold : threshold to determine transmembrane residue. [default = 0.5]
-k keep_file : keep the intermediate files if its value is 1 [default = 0]
-l real_label : real PDBTM Topology label file, in three lines [default = null]
-H home : home directory of PDBTM_Topology_Pred.sh
[default = ~/GitBucket/Predict_Property]
========
Example:
========
#-> 1. Predict_Property
./Predict_Property.sh -i example/1pazA.tgt
#-> 2. AUCpreD
./AUCpreD.sh -i example/T0530.tgt
#-> 3. PDBTM_Topology_Pred
./PDBTM_Topology_Pred.sh -i example/1bhaA.tgt
=============
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 Accessibility (ACC), Order/Disorder prediction (DISO), and TransMembrane topology (TM2 and TM8).
------------------
2. detailed results in separate files:
SeqID.ss3
SeqID.ss8
SeqID.acc
SeqID.tm2
SeqID.tm8
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.tm2_simp
SeqID.tm8_simp
SeqID.diso_simp
These files contain the simple prediction results in one line.
------------------