GPPIAL

README file for GPPIAL software. This software takes two networks as input and returns a global alignment of them.

CONTENTS:

1. GPPIAL tutorial

2. Input file format

3. Output file

4. GPPIAL tutorial : (1) Unzip the GPPIAL zip file and enter the directory GPPIAL; (2) Copy two input graph file into the directory you want under GPPIAL, and rename the smaller graph "graphA.txt", the bigger one "graphB.txt"; (3) Copy the sequence similarity file of the two input graph file into the same directory, and rename it "A-B.seqsim"; (4) Copy the functiom similarity file of the two input graph file into the same directory, and rename it "A-B.funsim"; (5) Copy the inparanoid file of the two input graph file into the same directory, and rename it "Inparanoid-A-B-geneIds"; (6) How to use: Usage: .\GPPIAL.exe graphA.txt graphB.txt A-B.seqsim A-B.funsim Inparanoid-A-B-geneIds [-a alpha] [-b beta] [-l lambda] [-g gamma] [-d delta] [-i it] options: -a alpha : balances sequence similarity and functional similarity (default 0.5, scale 0-1) -b beta : balances biological similarity and degree similarity (default 0.02, scale 0-1) -l lambda: balances the similarity of two nodes and their neighbor similarity (default 0.1, scale 0-1) -g gamma : balances node similarity and interaction score (default 0.001, scale 0-1) -d delta : the threshold to filter anchors (default 0.7, scale 0-1) -i it : defines the number of iterations for computing node similarities (default 2, non-negative integer number)

Example 1: .\GPPIAL.exe graphA.txt graphB.txt A-B.seqsim A-B.funsim Inparanoid-A-B-geneIds Exmaple 2: .\GPPIAL.exe graphA.txt graphB.txt A-B.seqsim A-B.funsim Inparanoid-A-B-geneIds -a 0.5 -b 0.01

2. Input file format : (1) graphA.txt : graph A. Each line corresponds to an interaction and contains the geneIds of two proteins (separated by a tab) in that interaction. (2) graphB.txt : graph B. Same format as graphA_ppi.tab. (3) A-B.seqsim : nomarlized sequence similarity file of graph A and graph B using BLAST. Each line consists of the geneIds of two proteins and the sequence similarity between them. (4) A-B.funsim : nomarlized function similarity file of graph A and graph B using Schlicker. Each line consists of the geneIds of two proteins and the function similarity between them. (5) Inparanoid-A-B-geneIds: orthologous protein pairs between A and B downloaded from Inparanoid database. Each line corresponds to one pair.

3. Output file: (1) graphA-go & graphB-go : GO terms file of graphA and graphB, respectively. Each line contains a protein and its GO terms. (2) Inparanoid-A-B-geneIds-filtered : anchors selected by matching construction step. (3) Inparanoid-A-B-geneIds-test : test set generated by matching construction step to further analyze the alignment quality. (4) graphA-graphB.alignment : the final matching result. It is a node pair list in the form of "nodeID in graph A nodeID in graph B". (5) graphA-graphB.align-evaluation : alignment evaluation results, showing parameters involved in GPPIAL, and topological and biological measures.

Contacts: Yuanyuan Zhu (yyzhu@whu.edu.cn) Yaoran Chen (yaoran_chen@whu.edu.cn) Ming Zhong (clock@whu.edu.cn) Rong Peng (rongpeng@whu.edu.cn) Juan Liu (liujuan@whu.edu.cn)