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Alignment using genetic programming with causal trees for identification of protein functions.

ABSTRACT: A hybrid evolutionary model is used to propose a hierarchical homology of protein sequences to identify protein functions systematically. The proposed model offers considerable potentials, considering the inconsistency of existing methods for predicting novel proteins. Because some novel proteins might align without meaningful conserved domains, maximizing the score of sequence alignment is not the best criterion for predicting protein functions. This work presents a decision model that can minimize the cost of making a decision for predicting protein functions using the hierarchical homologies. Particularly, the model has three characteristics: (i) it is a hybrid evolutionary model with multiple fitness functions that uses genetic programming to predict protein functions on a distantly related protein family, (ii) it incorporates modified robust point matching to accurately compare all feature points using the moment invariant and thin-plate spline theorems, and (iii) the hierarchical homologies holding up a novel protein sequence in the form of a causal tree can effectively demonstrate the relationship between proteins. This work describes the comparisons of nucleocapsid proteins from the putative polyprotein SARS virus and other coronaviruses in other hosts using the model.

SUBMITTER: Hung CM

PROVIDER: S-EPMC7117053 | biostudies-literature | 2006 Sep

REPOSITORIES: biostudies-literature

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Alignment using genetic programming with causal trees for identification of protein functions.

Hung Chun-Min CM Huang Yueh-Min YM Chang Ming-Shi MS

Nonlinear analysis, theory, methods & applications 20051128 5

A hybrid evolutionary model is used to propose a hierarchical homology of protein sequences to identify protein functions systematically. The proposed model offers considerable potentials, considering the inconsistency of existing methods for predicting novel proteins. Because some novel proteins might align without meaningful conserved domains, maximizing the score of sequence alignment is not the best criterion for predicting protein functions. This work presents a decision model that can mini ...[more]

PMID: 32288048

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Project description:BackgroundThe combination of genotypic and genome-wide expression data arising from segregating populations offers an unprecedented opportunity to model and dissect complex phenotypes. The immense potential offered by these data derives from the fact that genotypic variation is the sole source of perturbation and can therefore be used to reconcile changes in gene expression programs with the parental genotypes. To date, several methodologies have been developed for modeling eQTL data. These methods generally leverage genotypic data to resolve causal relationships among gene pairs implicated as associates in the expression data. In particular, leading studies have augmented Bayesian networks with genotypic data, providing a powerful framework for learning and modeling causal relationships. While these initial efforts have provided promising results, one major drawback associated with these methods is that they are generally limited to resolving causal orderings for transcripts most proximal to the genomic loci. In this manuscript, we present a probabilistic method capable of learning the causal relationships between transcripts at all levels in the network. We use the information provided by our method as a prior for Bayesian network structure learning, resulting in enhanced performance for gene network reconstruction.ResultsUsing established protocols to synthesize eQTL networks and corresponding data, we show that our method achieves improved performance over existing leading methods. For the goal of gene network reconstruction, our method achieves improvements in recall ranging from 20% to 90% across a broad range of precision levels and for datasets of varying sample sizes. Additionally, we show that the learned networks can be utilized for expression quantitative trait loci mapping, resulting in upwards of 10-fold increases in recall over traditional univariate mapping.ConclusionsUsing the information from our method as a prior for Bayesian network structure learning yields large improvements in accuracy for the tasks of gene network reconstruction and expression quantitative trait loci mapping. In particular, our method is effective for establishing causal relationships between transcripts located both proximally and distally from genomic loci.

Dataset Information

Alignment using genetic programming with causal trees for identification of protein functions.

Publications

Alignment using genetic programming with causal trees for identification of protein functions.

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