GraphAlignment
"GraphAlignment" introduces a method for analyzing the evolutionary relationships between interaction networks across species through network alignment. This approach is grounded in evolutionary biology and enables the identification of functional relationships between genes in diverse organisms. By considering both the interaction patterns within networks and the sequence similarities between nodes (genes or proteins), GraphAlignment employs a sophisticated scoring function to measure mutual similarities across species' networks.
The method stands out for its systematic Bayesian analysis, which is used to infer high-scoring alignments and determine optimal alignment parameters. This analytical rigor allows the discovery of conserved functional relationships that might not be apparent through sequence similarity alone.
Topic
Molecular interactions, pathways and networks;Gene expression
Detail
Operation: Pathway or network comparison
Software interface: Command-line user interface,Library
Language: R
License: -
Cost: Free
Version name: 1.66.0
Credit: Deutsche Forschungsgemeinschaft.
Input: -
Output: -
Contact: Joern P. Meier mail@ionflux.org
Collection: -
Maturity: Stable
Publications
- Cross-species analysis of biological networks by Bayesian alignment.
- Berg J and Lässig M. Cross-species analysis of biological networks by Bayesian alignment. Cross-species analysis of biological networks by Bayesian alignment. 2006; 103:10967-72. doi: 10.1073/pnas.0602294103
- https://doi.org/10.1073/pnas.0602294103
- PMID: 16835301
- PMC: PMC1544158
Download and documentation
Source: https://bioconductor.org/packages/release/bioc/src/contrib/GraphAlignment_1.66.0.tar.gz
Documentation: https://bioconductor.org/packages/release/bioc/manuals/GraphAlignment/man/GraphAlignment.pdf
Home page: http://bioconductor.org/packages/release/bioc/html/GraphAlignment.html
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