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DomainGraph

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Release 1.0, April 2008

System Requirements

The plugin works with Cytoscape 2.5 and 2.6, which requires Java SE 5 or Java SE 6.

Dataset Versions

Release 1.0 is based on UniProt version 12.8, Ensembl 47 and Pfam version 22.

Domain-Domain-Interaction Datasets:

Structural datasets:
  • iPfam version 21
  • 3did version of November 2007
Predicted datasets:
  • InterDom version 2.0
  • LLZ
  • DPEA
  • DIMA version 2.0, consisting of 3 subsets (domain profiling, DPEA, and string)
  • LDSC consisting of 2 sets: all interactions and a core subset
  • RDFF
  • RCDP50
  • APMM consisting of 2 sets: APMM1 and APMM2
  • LP
  • PINS
  • IPPRI (Schelhorn, S.E., Lengauer, T., Albrecht, M. (2008) An integrative approach for predicting interactions of protein regions. Bioinformatics, in press.)

Download

Download DomainGraph Release 1.0.

Contributors

Dorothea Emig1, Melissa S. Cline2, Thomas Lengauer1, and Mario Albrecht1
1 Department of Computational Biology & Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
2 Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, California, USA