Java Input Output

Input

The Graph can be created for all the Human proteins or for a custom protein list.

By default, no input is required and all Human proteins are used. If an input file is provided, it has to be a list of proteins represented by their Uniprot Accession number, one each line. Example:

P47211
O43603
O75325
P37288
Q8IWW8
Q9BZL3
P00736
P18505
P09871
P16118
P55317

The custom input file can be specified using the -i command line argument.

Output

The result graph is a ".sif" file, with the following structure:

protein1 <interaction type> protein2
protein3 <interaction type> protein1 
protein4 <interaction type> protein5 protein6 protein2
protein7
...

By default, the result ".sif" file will be in the same location as the ".jar" file by default. A different location can be selected using the -o command line argument.