GRAAL / C-GRAAL / MI-GRAAL/ L-GRAAL – Matching-based Integrative / GRAph ALigner

GRAAL / C-GRAAL / MI-GRAAL / L-GRAAL

:: DESCRIPTION

GRAAL aligns a pair of nodes originating in different networks based on a similarity measure of their local neighbourhoods

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C-GRAAL  (Common-neighbors based GRAph ALigner) is a novel pairwise global alignment algorithm that uses heuristics for maximizing the number of aligned edges between two networks and is based solely on network topology.

MI-GRAAL is a novel network alignment algorithm, which can integrate any number and type of similarity measures between network nodes (e.g. proteins), including, but not limited to, any topological network similarity measure, sequence similarity, functional similarity and structural similarity.

L-GRAAL (Lagrangian GRAphlet-based network Aligner) is a novel global network alignment tool, which combines an efficient solver based on Lagrangian relaxation with a scoring function based on the statistics of small induced subgraphs called graphlets.

::DEVELOPER

Nataša Pržulj, Imperial College

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 GRAAL / C-GRAAL / MI-GRAAL / L-GRAAL

:: MORE INFORMATION

Citation

L-GRAAL: Lagrangian Graphlet-based Network Aligner.
Malod-Dognin N, Pržulj N.
Bioinformatics. 2015 Feb 28. pii: btv130.

J R Soc Interface. 2010 Sep 6;7(50):1341-54. doi: 10.1098/rsif.2010.0063. Epub 2010 Mar 17.
Topological network alignment uncovers biological function and phylogeny.
Kuchaiev O, Milenkovic T, Memisevic V, Hayes W, Przulj N.

C-GRAAL: common-neighbors-based global GRAph ALignment of biological networks.
Memišević V, Pržulj N.
Integr Biol (Camb). 2012 Jul;4(7):734-43. doi: 10.1039/c2ib00140c.

Bioinformatics. 2011 May 15;27(10):1390-6. doi: 10.1093/bioinformatics/btr127. Epub 2011 Mar 16.
Integrative network alignment reveals large regions of global network similarity in yeast and human.
Kuchaiev O, Przulj N.