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BMC Bioinformatics. 2013;14 Suppl 15:S18. doi: 10.1186/1471-2105-14-S15-S18. Epub 2013 Oct 15.

Mapping proteins in the presence of paralogs using units of coevolution.

Abstract

BACKGROUND:

We study the problem of mapping proteins between two protein families in the presence of paralogs. This problem occurs as a difficult subproblem in coevolution-based computational approaches for protein-protein interaction prediction.

RESULTS:

Similar to prior approaches, our method is based on the idea that coevolution implies equal rates of sequence evolution among the interacting proteins, and we provide a first attempt to quantify this notion in a formal statistical manner. We call the units that are central to this quantification scheme the units of coevolution. A unit consists of two mapped protein pairs and its score quantifies the coevolution of the pairs. This quantification allows us to provide a maximum likelihood formulation of the paralog mapping problem and to cast it into a binary quadratic programming formulation.

CONCLUSION:

CUPID, our software tool based on a Lagrangian relaxation of this formulation, makes it, for the first time, possible to compute state-of-the-art quality pairings in a few minutes of runtime. In summary, we suggest a novel alternative to the earlier available approaches, which is statistically sound and computationally feasible.

PMID:
24564758
PMCID:
PMC3852051
DOI:
10.1186/1471-2105-14-S15-S18
[Indexed for MEDLINE]
Free PMC Article

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