Reconstituting protein interaction networks using parameter-dependent
domain-domain interactions

(Supplementary executable files)

Vesna Memišević, Anders Wallqvist, and Jaques Reifman

Department of Defense Biotechnology High Performance Computing Software Applications Institute,
Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command,
Fort Detrick, MD 21702

Corresponding author. Tel.: +1 301 619 7915; Fax: +1 301 619 1983.

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Parameter dependent DDI selection (PADDS)

Files:



How to run:





































  • Download and unpack PADDS program and a set of examples using the link above. Current version of the program is compiled on Unix64 machines. For different version, please contact the authors.
  • Run "./PADDS_unix64" without any parameters and it will display usage directions
  • Usage directions:
    "./PADDS_unix64 PPI_net.txt protin_domain_annotation.txt alpha output1.file output2.file (loops)"
  • Where:
    •   "PPI_net.txt" represents PPI network in the edge list format. E.g.,

      PROTEIN1    PROTEIN2
      PROTEIN1    PROTEIN3
      PROTEIN2    PROTEIN5
                         …
    • "protin_domain_annotation.txt" represents a list of protein-domain annotation mapping. E.g.,

      PROTEIN1    DOMAIN1
      PROTEIN1    DOMAIN2
      PROTEIN2    DOMAIN3
                         …
    • Protein names in the protein-domain annotation file have to match names of proteins in the PPI network.
    •  "alpha" represents a parameter in [0.0, 0.1] that specifies the amount of tolerable false positives (0.0 – tolerate larger number of false positives, 1.0 – do not tolerate large number of false positives)
    • "output1.file" contain a list of DDIs that explain a given set of PPIs. E.g.,

      DOMAIN1    DOMAIN5
      DOMAIN3    DOMAIN3
                         …
    • "output2.file" contain a list of DDIs that explain a given set of PPIs, as well as the original benefit value for each of the DDIs. E.g.,

      DOMAIN1    DOMAIN5     0.84
      DOMAIN3    DOMAIN3     0.92
                         …
    • "loops" represents an optional, user specified, parameter that tells program whether or not to include self-loops (PROTEIN1 - PROTEIN1) into analysis.
Example:










  • Download and unpack PADDS program and a set of examples using the link above, then run as:

1. No self-loops:

./PADDS_unix64 yeast_PPI_example.txt yeast_domains_example.txt 0.1 yeast_01_ddis.txt yeast_01_ddis_bf.txt

2. With self-loops:

./PADDS_unix64 yeast_PPI_example.txt yeast_domains_example.txt 0.1 yeast_01_ddis_sl.txt yeast_01_ddis_bf_sl.txt loops

Cite as:

  • Memišević V., Wallqvist A., and Reifman J.: Reconstituting protein interaction networks using parameter-dependent domain-domain interactions. BMC Bioinformatics 2013 14:154.

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Last update: 05/21/2013