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PROGRAM:NetCoffee2
AUTHOR:JIALU HU and JUNHAO HE
EMAIL: jhu@nwpu.edu.cn junhao.he@nwpu-bioinformatics.com
Copyright (C++) <2018>
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
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Description This file is README file of the package of NetCoffee2, developed by Junhao He. To guide you quickly starting to use our alignment tool, we structured this README into four parts:
- PREREQUISITE
- COMPILING
- OPTION
- EXAMPLE Before running this program, you are strongly recommended to read this file carefully.
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PREREQUISITE
Igraph-0.7.1 Igraph is a collection of network analysis tools with the emphasis on efficiency,portablity and ease of use. Igraph is open source and free.
The source code is freely available at website: http://igraph.org/c/#downloads.
Please first install igraph before compiling the code of NetCoffee2.
For detials in website: http://igraph.org/c/
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COMPLING
To compile the source code, the latest compilers which supports the standard language C++11, also known as C++0x, is needed. Other older compiler may not support it.
cd $NETCOFFEE2
./make MODE=Release
#If you want to compile it in Debug mode, run command:
./make (MODE=Debug)
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OPTION
You can see the detailed option information with option "-help".
It is noted that there are four options you must specify if you want to run NetCoffee2 for an alignment task. They are described as follows:
- -inputnet
This option specifies the file name of several networks you want to align.
It is ecpected to be in three-column tab-delimited format.
First column: netID
second column: interactorA
third column: interactorB
For example, suppose we have three PPI networks:homoSapiens, MusMusculus,DrosophilaMelanogaster. The inputnet file should looks like:
-----------------------BEGIN OF INPUTNET---------------------
HomoSapiens P62633 Q00577
HomoSapiens Q9GZT8 Q2VPB7
HomoSapiens O95602 P04626
HomoSapiens P56524 Q08379
MusMusculus P10605 P11438
MusMusculus P03966 Q6PDN3
MusMusculus Q9DBY1 P57716
MusMusculus Q9WUD1 Q61083
DroMelanogaster Q7KSX2 Q7KSX2
DroMelanogaster Q9VKA1 Q9VX51
DroMelanogaster Q9BN17 Q9VD53
DroMelanogaster O61492 A1ZAZ2
-------------------------END OF INPUTNET----------------------
- -inputbit
This option specifies the blastp sequence similarity files for each pair of species, which includes three columns seperated by . The first column provides proteins from the first netwoks, the second column provides proteins from the second networks, the third column provides bitscore. Here is an example:
--------------BEGIN OF BITSCORE FILE--------------
Q9V406 Q9D030 3.88e-04 42.0
Q9VV77 Q9I7U7 0.054 35.0
Q9VF55 Q39244 2.6 29.6
Q8RYD9 Q60929 1.30e-13 70.5
P40301 O81147 1.34e-38 134.0
Q9VJQ5 Q84W66 3.77e-15 71.2
Q9VCZ4 Q06831 2.05e-04 40.0
Q6IMB1 O18335 2.58e-15 72.8
--------------END OF BITSCORE FILE--------------
- -numnet
This option tell program how many networks you want to align.
- -output
This option tell program the name and path of result of alignment and alignment score, by default, it is in result folder
- other option in Usage
You can generate the follow message by running the program with option "-help"
$NETCOFFEE2/bin/NetCoffee2 -help
USAGE: NetCoffee2 [-help] [-beta DOUBLE] [-version] -numnet INTEGER -inputbit STRING -inputnet STRING -output STRING [-alph DOUBLE] [-evalue DOUBLE]
DESCRIPTION: An application for multiple global network alignment.
VERSION: NetCoffee2 1.0.006
ALL MANDATORY AND OPTIONAL ARGUMENTS:
-evalue evalue used to pick the sequence similarity which has a lower e-value than evalue, default=1e-7
-alph alph for sequence and topology similarity
-beta beta used for the rate of conserved protein in a same network, default=0
-output A mandatory option. The path of an output file.
-numnet A mandatory option. The number of ppi networks
-help Show help information.
-version Show the current version.
-inputbit A mandatory option. The path of an input file.
-beta beta used for the rate of conserved protein in a same network
-alph alph for sequence and topology similarity， default=0.5
-inputnet A mandatory option. The path of an input file.
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EXAMPLE
- Download dataset
Our datasets are freely available at our website: http://www.nwpu-bioinformatics.com/
Download it into the folder of $NETCOFFEE2 and uncompress it with command:
tar -zxvf dataset.tar.gz
- Dataset Description
By download dataset in our website, you will have three test data, two of which have three real PPI networks(test1, test2). and the other is a simple example of two small nets for NetCoffee2(test_sample).
- Compile source code
Compile the source code with command:
make MODE=Release
- Run NetCoffee2 on our test dataset with commend:
./NetCoffee2 -inputnet ./testdata/test2/int_net_test2.txt -inputbit ./testdata/test2/int_bit_test2.txt -output "alignmentResule.txt" -numnet 3
Then you can find the alignment result and alignment score in result folder.
There are many other functions which you can see with "-help" option
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END
THANK FOR READING
If you have any questions regarding to the program, please don't hesitate to contact us through email.