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Review
. 2015 Sep 3:51:4.12.1-4.12.8.
doi: 10.1002/0471250953.bi0412s51.

Protein Function Prediction: Problems and Pitfalls

William R Pearson  1
Affiliations
Review

Protein Function Prediction: Problems and Pitfalls

William R Pearson. Curr Protoc Bioinformatics. .

Abstract

The characterization of new genomes based on their protein sets has been revolutionized by new sequencing technologies, but biologists seeking to exploit new sequence information are often frustrated by the challenges associated with accurately assigning biological functions to newly identified proteins. Here, we highlight some of the challenges in functional inference from sequence similarity. Investigators can improve the accuracy of function prediction by (1) being conservative about the evolutionary distance to a protein of known function; (2) considering the ambiguous meaning of "functional similarity," and (3) being aware of the limitations of annotations in functional databases. Protein function prediction does not offer "one-size-fits-all" solutions. Prediction strategies work better when the idiosyncrasies of function and functional annotation are better understood.

Keywords: EC numbers; function prediction; gene ontology; homology; orthology; paralogy.

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References

Literature Cited

    1. Gene Ontology Consortium 2001. Creating the gene ontology resource: Design and implementation. Genome Res. 11:1425-1433. doi: 10.1101/gr.180801.
    1. Gene Ontology Consortium 2014. Guide to GO evidence codes (http://geneontology.org/page/guide-go-evidence-codes).
    1. Altenhoff, A.M. , Studer, R.A. , Robinson-Rechavi, M. , and Dessimoz, C. 2012. Resolving the ortholog conjecture: Orthologs tend to be weakly, but significantly, more similar in function than paralogs. PLoS Comput. Biol. 8:e1002514. doi: 10.1371/journal.pcbi.1002514.
    1. Altschul, S.F. , Madden, T.L. , Schaffer, A.A. , Zhang, J. , Zhang, Z. , Miller, W. , and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402. doi: 10.1093/nar/25.17.3389.
    1. Blake, J.A. and Harris, M.A. 2008. The gene ontology (GO) project: Structured vocabularies for molecular biology and their application to genome and expression analysis. Curr. Protoc. Bioinform. 23:7.2:7.2.1-7.2.9.

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