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J Proteome Res. 2008 Jan;7(1):192-201. Epub 2007 Dec 15.

Data augmentation algorithms for detecting conserved domains in protein sequences: a comparative study.

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Bioinformatics and Intelligent Computing Lab, Children's Mercy Hospitals and Clinics Schools of Medicine, Computing and Engineering University of Missouri, Kansas City, Missouri 64108, USA.


Protein conserved domains are distinct units of molecular structure, usually associated with particular aspects of molecular function such as catalysis or binding. These conserved subsequences are often unobserved and thus in need of detection. Motif discovery methods can be used to find these unobserved domains given a set of sequences. This paper presents the data augmentation (DA) framework that unifies a suite of motif-finding algorithms through maximizing the same likelihood function by imputing the unobserved data. The data augmentation refers to those methods that formulate iterative optimization by exploiting the unobserved data. Two categories of maximum likelihood based motif-finding algorithms are illustrated under the DA framework. The first is the deterministic algorithms that are to maximize the likelihood function by performing an iteratively optimal local search in the alignment space. The second is the stochastic algorithms that are to iteratively draw motif location samples via Monte Carlo simulation and simultaneously keep track of the superior solution with the best likelihood. As a result, four DA motif discovery algorithms are described, evaluated, and compared by aligning real and simulated protein sequences.

[Indexed for MEDLINE]

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