all-vs-all blastp to network diagrams

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Ryan G

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Apr 5, 2016, 6:52:14 PM4/5/16
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Hello,

I am completely new to Cytoscape, and don't really know how to do what I want, or if Cytoscape does what I'm hoping it does. I have carried out an all-vs-all blastp analysis for 7 eukaryotic species - this was used subsequently for an OrthoMCL analysis of protein groups in these species. What I'm hoping to do is use the blastp output (or even better, the final OrthoMCL groups) and generate network diagrams that depict gene family expansion and/or reduction. I am running this on my Macbook (10.11.2) with 16 GB of RAM.

I noticed a package for Cytoscape called BLAST2SimilarityGraph, but I didn't realize that the package doesn't work with the version of Cytoscape that I've downloaded (3.3). So I'm wondering a couple of things: 1) Do I have to download the old version of Cytoscape and install BLAST2SimilarityGraph? and 2) How might I go about doing this analysis with Cytoscape 3.3, if it is possible? Are there other packages to download that might help?

Thanks in advance!
Ryan 

Scooter Morris

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Apr 5, 2016, 7:21:33 PM4/5/16
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Hi Ryan,
    There are several ways to import networks into Cytoscape.  Unfortunately, the OrthoMCL output doesn't include any similarity values, so while you could use it to define groups, it wouldn't be very useful.  It's actually pretty easy to turn your all-by-all BLAST results into a file to import into Cytoscape, though.  All you need is something like:

protein1 protein2 similarity

where we usually use -log of the E-Value for the similarity.

-- scooter
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Ryan G

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Apr 5, 2016, 7:26:05 PM4/5/16
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Thanks, Scooter. Ok, I had done essentially as you said, except that I hadn't made a -log of my evalue. So, does the import of the table into Cytoscape (which takes quite a while on my computer) automatically generate the kind of information that I'm looking for? Or do I have to run it through some other application within Cytoscape to get the sorts of visual depictions that I'm after?

Thanks again,
Ryan

Scooter Morris

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Apr 5, 2016, 7:53:42 PM4/5/16
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On 04/05/2016 04:26 PM, Ryan G wrote:
Thanks, Scooter. Ok, I had done essentially as you said, except that I hadn't made a -log of my evalue. So, does the import of the table into Cytoscape (which takes quite a while on my computer) automatically generate the kind of information that I'm looking for? Or do I have to run it through some other application within Cytoscape to get the sorts of visual depictions that I'm after?
Well, I'm not sure what visual depictions you after, but if you import the network and then use an edge-weighted layout, you should get a pretty reasonable similarity network.

-- scooter


Thanks again,
Ryan

On Tuesday, April 5, 2016 at 3:52:14 PM UTC-7, Ryan G wrote:
Hello,

I am completely new to Cytoscape, and don't really know how to do what I want, or if Cytoscape does what I'm hoping it does. I have carried out an all-vs-all blastp analysis for 7 eukaryotic species - this was used subsequently for an OrthoMCL analysis of protein groups in these species. What I'm hoping to do is use the blastp output (or even better, the final OrthoMCL groups) and generate network diagrams that depict gene family expansion and/or reduction. I am running this on my Macbook (10.11.2) with 16 GB of RAM.

I noticed a package for Cytoscape called BLAST2SimilarityGraph, but I didn't realize that the package doesn't work with the version of Cytoscape that I've downloaded (3.3). So I'm wondering a couple of things: 1) Do I have to download the old version of Cytoscape and install BLAST2SimilarityGraph? and 2) How might I go about doing this analysis with Cytoscape 3.3, if it is possible? Are there other packages to download that might help?

Thanks in advance!
Ryan 
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