Abstract
We employ a novel method to construct a phylogenetic tree based on distance matrix among different protein molecular sequences, and present a statistical model to infer specific molecular function for unannotated protein sequences within the phylogenetic tree. Our method produced specific and consistent molecular function prediction across the P-falciparum family. For the P-falciparum family, it achieves 91.2% precision and 76.9% recall, outperforms the related method GOtcha and BLAST. Finally, we intend to improve our method through adopting a more appropriate feature extraction approach from the sequence or a better statistical inference model in the future.
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References
Eisen, J.A.: Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis. Genome Research (8), 163–167 (1998)
Barbara, E.E., Michael, I.J., Kathryn, E.M.: Protein Molecular Function Prediction by Bayesian Phylogenomics. PLoS Computational Biology 1(5), e45 (2005)
Barbara, E.E., Michael, I.J., Kathryn, E.M.: A Graphical Model for Predicting Protein Molecular Function. In: ICML, Pittsburgh (2006)
Eisen, J.A., Hanawalt, P.C.: A Phylogenomics Study of DNA Repair Genes, proteins, and Processes. Mutation Research (3), 171–213 (1999)
Shen, J., Zhang, J., Luo, X.: Predicting Protein–protein Interactions Based Only on Sequences Information. Proceedings of the National Academy of Sciences 104(11), 4337–4341 (2007)
Camon, E.: The Gene Ontology Annotation (GOA) Database: Sharing Knowledge in Uniprot with Gene Ontology. Nucleic Acids Research (32), 262–266 (2004)
Jukes, T.H., Cantor, C.R.: Evolution of Protein Molecules. Mammalian protein metabolism, pp. 21–132. Academic Press, New York (1969)
Pearl, J.: Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference, p. 531. Morgan Kaufmann (1988)
Cowell, R.G., Dawid, A.P., Lauritzen, S.L.: Probabilistic Networks and Expert System, 321 p. Springer, New York (2003)
Karaoz, U., Murail, T.M., Letovsky, S.: Whole-genome Annotation by Using Evidence Intergration in Functional-linkage Networks. Proceedings of the National Academy of Sciences 101, 2888–2893 (2004)
Martin, D.M.A.: GOtcha: A New Method for Prediction of Protein Function Assessed by the Annotation of Seven Genomes. BMC Bioinformatics (5), 178–195 (2004)
Altschul, S.F.: Basic Local Alignment Search Tool. J. Mol. Biol. (215), 403–410 (1990)
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Jian, L. (2012). Protein Molecular Function Prediction Based on the Phylogenetic Tree. In: Huang, DS., Gupta, P., Zhang, X., Premaratne, P. (eds) Emerging Intelligent Computing Technology and Applications. ICIC 2012. Communications in Computer and Information Science, vol 304. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31837-5_27
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DOI: https://doi.org/10.1007/978-3-642-31837-5_27
Publisher Name: Springer, Berlin, Heidelberg
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