Optimizing a global alignment of protein interaction networks.

ABSTRACT:

Motivation

The global alignment of protein interaction networks is a widely studied problem. It is an important first step in understanding the relationship between the proteins in different species and identifying functional orthologs. Furthermore, it can provide useful insights into the species' evolution.

Results

We propose a novel algorithm, PISwap, for optimizing global pairwise alignments of protein interaction networks, based on a local optimization heuristic that has previously demonstrated its effectiveness for a variety of other intractable problems. PISwap can begin with different types of network alignment approaches and then iteratively adjust the initial alignments by incorporating network topology information, trading it off for sequence information. In practi

SUBMITTER: Chindelevitch L 

PROVIDER: S-EPMC3799479 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature