Encyclopedia of Systems Biology

2013 Edition
| Editors: Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota

Parameter Estimation, Graph Alignment

Reference work entry
DOI: https://doi.org/10.1007/978-1-4419-9863-7_994

Synonyms

Definition

Parameter estimation is a process of finding an appropriate set of parameters for the scoring function of the graph alignment problem ( Scoring Function, Graph Alignment). These parameters serve the same purpose as the scoring matrices of the Sequence Alignment (e.g., PAM or BLOSUM ( BLOcks SUbstitution Matrix (BLOSUM))). The scoring parameters are estimated for both the node score ( Node Score, Graph Alignment) and the link score ( Link Score, Graph Alignment) and they ultimately weigh the relative contributions of topological and sequence similarity to the score ( Scoring Function, Graph Alignment).

The early parameter estimates were determined ad hoc and allowed only limited application of the graph alignment ( Graph Alignment, Protein Interaction Networks) (e.g., motif search ( Network Motif), pathway querying ( Pathway), and an alignment based solely on the protein similarity). With an increased availability of the...

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References

  1. Berg J, Lässig M (2006) Cross-species analysis of biological networks by Bayesian alignment. Proc Natl Acad Sci USA 103(29):10967–10972PubMedGoogle Scholar
  2. Flannick J, Novak A, Srinivasan BS, McAdams HH, Batzoglou S (2006) Græmlin: general and robust alignment of multiple large interaction networks. Genome Res 16:1169–1181PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  1. 1.Institute of Molecular Genetics, Academy of Sciences of the Czech RepublicPragueCzech Republic