Sequence Similarity Network - Cytoscape 3.0

[E]

A couple years back I was working with Cytoscape 2.7XXX to make protein sequence similarity networks based on BLAST E values. Basically we would download FASTA files--> AllByAll BLAST --> Use BLAST2SimilarityGraph input the fasta file and the BLAST file--> generates sequence similarity network. 

I was hoping someone might be able to give me some assistance on how to do such a thing in Cytoscape 3.0

Thanks!

EH

[Scooter Morris]

Hi EH,
    Sure, from my recollection all BLAST2SimilarityGraph did was to read the blast output and give you a network file.  Should be very easy to do with the blast file.  Not sure what it did with the original FASTA file -- maybe it was used to store the sequence.  In any case, the same thing should be possible with a little bit of Python.  What you want on the output is simply:

ID1\tID2\tBLAST E-Value

where \t is tab a character.   Then you can use the Cytoscape File->Import->Network->From File to create your network.

-- scooter

[Robert Rentzsch]

Hi!

Also, adding to Scooter's more direct answer, have you tried using the EFI-EST server? I was in the same situation you're in (or were, in 2015) and, IMO, it's become unneccessary to do it yourself having this flexible tool. It's quite fast too, which saves local resources.

http://efi.igb.illinois.edu/efi-est/

Best,
Rob