C-GRAAL: Common neighbors based global GRAph ALignment algorithm

(Supplementary material)


Vesna Memisevic and Natasa Przulj

Corresponding author: Prof. Natasa Przulj, e-mail: natasa [AT] cs.ucl.ac.uk

  • About:
    • V.Memišević and N. Pržulj, “C–GRAAL: Common–Neighbors–Based Global GRAph ALignment of Biological Networks,”
      Integr. Biol., 4:734-743, 2012. PMCID: 22234340
    • Supplementary Material
  • Executables:
  • Networks:
  • Alignments:
  • Predictions:

    • How to run C-GRAAL:

    • Download and unpack the C-GRAAL using the link above.
    • C-GRAAL accepts networks in LEDA .gw format.
    • Run "./CGRAAL_unix64" without any parameters and it will display usage directions

    • Usage directions:"./CGRAAL_unix64 net1.gw net2.gw similarity.file output1.file output2.file", where:
      • "net1.gw" - first network (gw format)
      • "net2.gw" - second network (gw format)
      • "similarity.file": similarity between nodes in net1 and net2 in the following format: nodeXNet1 nodeYNet2 similarity
      • "output1.file" - alignment output file in following format: node_Net1 (aligned to) node_Net2, where nodes are represented as node numbers
      • "output2.file" - alignment output file in following format: node_Net1 (aligned to) node_Net2, where nodes are represented as node names
    • Note: Number of nodes in the first network must not be greater than number of nodes in the second network!

    How to convert network from edge list format to .gw file accepted by C-GRAAL:

    If your network is in edge list format:

    node1 node2
    node3 node4
    ...
    You can use "list2leda" script (part of "CGRAAL_unix64.zip") to convert it into the format accepted by C-GRAAL.
    Use it like this: "./list2leda edgelist.txt >> graph.gw"
    Note that self-loops, directionality and double edges will be ignored.

    Figures:

    The largest common connected component of the best yeast-human alignmentThe largest common connected component of the best C. jejuni-E. coli alignmentThe largest common connected component of the best Mesorhizobium loti-Synechocystis sp PCC6803 alignment
    The largest common connected component of the best yeast-human alignment
    The largest common connected component of the best C. jejuni-E. coli alignment
    The largest common connected component of the best Mesorhizobium loti-Synechocystis sp PCC6803 alignment
    The largest common connected component of the best F.tularensis - H.sapiens alignmentThe largest common connected component of the best B.anthracis - H.sapiens alignmentThe largest common connected component of the best Y.pestis - H.sapiens alignment
    The largest common connected component of the best F.tularensis - H.sapiens alignment
    The largest common connected component of the best B.anthracis - H.sapiens alignment
    The largest common connected component of the best Y.pestis - H.sapiens alignment

    Other network alignment algorithms:

        Notes:

    • All p-values presented in this paper were calculated using Matlab 2007. Newer Matlab versions use a different output precision format
      and consequently, it is possible that the p-values obtained by the newer versions will differ from those obtained by the version 2007
      (e.g., old version p-value: 1.7E-9, newer version p-value: 0.0).
    Last update: 04/25/2013