Alternatives to Broad's DAPPLE tool?

Question

[sic]

Hi everyone

I have a set of coding variants, on which I want to run some protein protein interaction tools. I've used a couple of resources so far (String, CPDB), and I really want to use Broad's (online) DAPPLE tool. Unfortunately it's been down for some time now, and I can't get a hold of the tool's developers, nor can I find any sources to download so I can run it locally.

My questions - is there anyone here that has used this tool? Could anyone recommend a similar tool, or does anyone have source I could install/run locally?

For reference I've attached a link to a figure generated by DAPPLE, from Neale et al's 2012 article "Patterns and rates of exonic de novo mutations in autism spectrum disorders":

Thank you!

[Leandro Lima]

Hi sic.

What type of analysis exactly you want to do?

As far as I know, DAPPLE gets a list of genes or SNPs and creates the PPI network of the proteins involved with these sets. I'd recommend you to try Cytoscape apps.

Leandro

Answer 1

[avigailtaylor]

Hi Sic,

You could try GeneNet Toolbox for MATLAB. I am the author of this toolbox, and it is available at:

http://avigailtaylor.github.io/gntat14/

Hope this helps.

Avigail