NetAl Help

 

NetWork Alignment ( Beta version )

The program gives two network as inputs and returns a global alignment.

Here is a template for running the program:

./NETAL net1 net2 [-a av] [-b bv] [-c cv] [-i iv]

Here is an example of running the program:

./NETAL yeast human -a 0.0001 -b 0.6 -c 0.5 -i 2

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net1: Name of the first network
net2: Name of the second network

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Input Files 

You should provide files “net1.tab” and “net2.tab” with following rules:

1- Files should be tab-separated.
2- Each line contains an interaction.
3- Each line starts with a string as the name of a protein in the interaction followed by a tab and a string as the name of another protein in the interaction.

Here is a sample for “net1.tab” :

node1 node2
node1 node3
node2 node4
node5 node6

If you want to use biological similarity data for proteins, you should provide files “net1-net1.val”,”net2-net2.val” and “net1-net2.val” with following rules:

1- Files should be tab-separated.
2- In “net1-net2.val” Each line starts with two strings and ends with a value. The first string is a name of a protein in net1. The second string which is separated by a tab is a name of a protein in net2. The value at the end of the line which is separated from second string by a tab is a float number that is a measurement for similarity between the first protein and the second one.
3- In “net1-net1.val” and “net2-net2.val” each line starts with a string as the name of a protein. In the second column you need to repeat the name. In the third column there is float number which is used to scale similarity of other proteins this one. ( fromnode to node edgeweight )

Here is a sample for “net1-net2.val”

aa ab 65.0
bb dd 32.4
ab cd 23.6

Here is a sample for “net1-net1.val”

aa aa 128.0
bb bb 94.7
ab ab 30.5

Output Files:

The program outputs two files “net1-net2.algn” and “net1-net2.eval”. The first one contains global alignment of two networks, each matched pair in a line, and the later contains some statistical of the alignment.