visualizing all-vs-all blast

[sofia...@gmail.com]

Hi,

I am trying to visualise my all-vs-all blast with cytoscape. It seems when I just upload my tab with the results from the blast that I get the network (without even telling in which column the blast score is). I just wanted to make sure that what I get is correct. Some people change the e-value to -log(e-value) before uploading the tab to cytoscape. What should I do ?

Another question : Is there a new alternative to the former app Blast2SimilarityGraph ?

Thank you very much in advance,
Sofia

[Scooter Morris]

Hi Sofia,

    Not sure what format you are using for your BLAST output, but all
you should really need is the query ID (source node), subject ID (target
node) and the e-value.  You shouldn't need to take the -log of your
e-value, although it might make it easier to do cutoffs.  If you do an
edge-weighted layout, make sure to go to the Settings dialog and set
-log for the edge weight interpretation, though.

-- scooter

[Sofia Rigou]

Thank you very much. I have all that and also other columns. So I enter the source and the target sequence but I can not check the e-value as the column for interaction type. Is that needed or does cytoscape recognize the e-value by it self ? 

Best regards, 

Sofia

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[Scooter Morris]

Just leave the e-value as an edge column (the default).

-- scooter

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[Sofia Rigou]

OK thank you very much!

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