Cytoscape is a truly wonderful tool for viewing sequence similarity networks. The only thing I don't love about it is that it's difficult to get selected sequences out of the network and into a FastA file for other types of analyses. I developed a kludgy Excel table where I copy-paste the information from the table panel at the bottom of the Cytoscape window and the Excel table combines and edits the Description and Sequence columns into FastA format. Am I missing some simpler method for doing this? If not, I suggest to Cytoscape developers that export-to-FastA would be a useful functionality to consider adding.
Indeed, we do monitor Biostars :-)
Where are you getting your sequence similarity network? If the network already has the sequences in a column, you should be able to export the table to a file and then read it directly into Excel. That will at least save you the cutting and pasting step. If you want to do this in a more automated fashion, there are two approaches you could take:
- An app would be pretty easy to write, but it would have to be in Java. There are lots of examples to get started if you know a Java programmer.
- Use Cytoscape automation and write a python or R module that reads the node table from Cytoscape and writes it out as a FASTA. This should be pretty simple to write (Biopython has a write method in the SeqIO package, for example) and would probably be only 10 or 15 lines of python.
Hope this helps!