how to add node scores beteen two network when using sana?

[xphuang2017]

Hi,
I'm going to use sana to solve network alignment. But, I don't know how to add the node similarities between two networks!
./sana -g1 A -g2 B -s3 0.5 -sequence 0.5
The command above is the usage of network alignment of A and B in the form of topology only, how can I add the node similarity(like Blast) between A and B?

[waynebhayes]

You can get useful online help inside SANA itself by typing "./sana -h | less", and then search for sequence. Let me know if that doesn't work. use [email protected].

…

-- Wayne Hayes, Ph.D. Associate Professor of Computer Science, University of California, Irvine Director, UCI-SDSU Joint Ph.D. Program in Computational Science (UCI side) *The evidence is now incontrovertible that Russia interfered with the 2016 US Presidential election by subtly manipulating public opinion via fake social media accounts. Why? Follow the money: Trump has been laundering it for Russian billionaires, including Putin, for 20 years. Details and fact checking at https://secure.avaaz.org/campaign/en/shocking_truth_about_trump/?bebhylb <https://secure.avaaz.org/campaign/en/shocking_truth_about_trump/?bebhylb>.* The opinions expressed in this email by Professor Hayes are his and his alone, and are not meant to represent those of the University of California.

On Tue, Jan 8, 2019 at 10:51 PM xphuang2017 ***@***.***> wrote: Hi, I'm going to use sana to solve network alignment. But, I don't know how to add the node similarities between two networks! ./sana -g1 A -g2 B -s3 0.5 -sequence 0.5 The command above is the usage of network alignment of A and B in the form of topology only, how can I add the node similarity(like Blast) between A and B? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#54>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ATUkjJf1_mfAMfjAbC3PrgqbcrMNoLuDks5vBZFJgaJpZM4Z24BP> .

[xphuang2017]

Great thanks to Professor Wayne Hayes! the command below can be used to add similarities:
./sana -g1 A -g2 B -s3 0.5 -simFile 1 AB.txt -esim 1 0.5 -simFormat 1 1

[skyblue0807]

Dear,
I also hope to use my own node similarity scores to align networks.
But I cannot find any contents about -simFile, -esim, -simFormat.
When I use similar command, I've got error message like below;

"Initializing measures...
1
AB.txt 1
Computing autogenerated/matrices/esim/yeast_human_esim_AB.txt ... ExternalSimMatrix: Error opening file"

Can anyone give me some help about these options?

[waynebhayes]

Apologies. I admit the instructions are not too clear.

The best-supported method is the 3-column method: G1node G2node SIM
where G1node is the name of a node in G1, G2node is the name of a node in G2, and SIM is a similarity value in [0.1]. I've added such a file for yeast-human to the repo (SANA2 branch), and once you "git pull" from that, you can try the below command (note the sim file is compressed but SANA knows how to decompress it):

./sana -g1 yeast -g2 human -ec 0.5 -esim 1 0.5 -simFile 1 sequence/yeast-human.simple.xz -simFormat 1 1

The meaning of the sim file argumnets are:

1. the "-esim" argument expects an integer (representing the number of SIM files you want to use, in this case just 1), followed by the WEIGHT to be assigned to that simfile (in this case 0.5, because we're also going to use the EC objective with weight 0.5).

2. the "-simFile" argument needs the same integer (1) that you provided to "-esim", followed by the name of the similarity file

3. the "-simFormat" expects again the number of simfiles (1), and then the FORMAT of each (which can be different if there was more than one). In this case it's format type 1, which is as described above: two node names followed by their similarity.