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Huynen et al. (2000, Genome Res) benchmarked different non-homology methods for function predictions using known functional relationships in the minimal M. genitalium genome, including physical interactions, metabolic pathways, regulatory relationships etc. Something along these lines would be more satisfactory than simply extracting individual model examples as benchmarks.
Within the application literature, neuro-fuzzy systems can be found as methods for function identification.
Network-based methods for function prediction have been comprehensively reviewed [10].
Computational methods for function recognition require far less time and expense and so can augment experimental methods.
Traditional experimental methods for function characterization cannot cope with the rate at which genomics efforts are generating data.
Despite this huge amount of data and the profusion of bioinformatic methods for function prediction, a large part of known enzyme activities is still lacking an associated protein sequence.
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The need to conduct experimental studies is determined both by the novelty of the proposed check valve design and by absence of verified computational validation methods for functioning of this type of valves.
Meanwhile, to validate the effectiveness of the method for function enrichment, the proteins in PIN with known functional categories were applied by the same PIN-based prediction procedure and we obtained corresponding 4,621 protein-function pairs containing total 2,274 proteins and 221 relative functional categories (GO terms).
We propose a doubly stochastic radial basis function (DSRBF) method for function recoveries.
The nlminb is a derivative-free method for function minimization as it requires only the function to be evaluated.
A new method for function estimation and variable selection, specifically designed for additive models fitted by cubic splines is proposed.
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