Abstract
Sequence alignment has been a commonly adopted technique for annotating gene functions. Biologists typically infer the function of a unknown query gene according to the function of the reference subject gene that shows the highest homology (commonly referred to as the “top hit”). BLAST search against the NCBI NR database has been the de facto “golden companion” in many applications. However, the NR database is known as noisy and contains significant sequence redundancy, which leads to various complications in the annotation process. This paper proposes an integrative approach that encompasses natural language processing (NLP) for feature representation of functional descriptions and a novel artificial neural network customized based on the Adaptive Resonance Associative Map (ARAM) for clustering of subject genes and for reducing their redundancy. The proposed approach was evaluated in a model legume species Medicago truncatula and was shown highly effective in our experiments.
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References
Dasarathy, B.V. (ed.): Nearest neighbor (NN) norms: NN pattern classification techniques. IEEE Computer Society, Los Alamitos (1990)
Pruitt, K.D., Tatusova, T., Maglott, D.R.: NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Research Database Issue, D61–D65 (2007)
The UniProt Consortium: The universal protein resource (UniProt) 2009. Nucleic Acids Research Database Issue, D169–D174 (2009)
Lewis, D.D.: Naive (Bayes) at forty: The independence assumption in information retrieval. In: Nédellec, C., Rouveirol, C. (eds.) ECML 1998. LNCS, vol. 1398, pp. 4–15. Springer, Heidelberg (1998)
Porter, M.: An algorithm for suffix stripping. Program 14(3), 130–137 (1980)
Robertson, S.: Understanding inverse document frequency: On theoretical arguments for IDF. Journal of Documentation 60(5), 503–520 (2004)
Carpenter, G., Grossberg, S.: ART 2: Self-organization of stable category recognition codes for analog input patterns. Applied Optics 26, 4919–4930 (1987)
Tan, A.: Adaptive Resonance Associative Map. Neural Networks 8(3), 437–446 (1995)
Carpenter, G., Grossberg, S.: A massively parallel architecture for a self-organizing neural pattern recognition machine. Computer Vision, Graphics, and Image processing 34, 54–115 (1987)
Carpenter, G.A., Grossberg, S., Reynolds, J.: ARTMAP: Supervised real-time learning and classification of nonstationary data by a self-organizing neural network. Neural Networks 4, 565–588 (1991)
Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., Sherlock, G.: Gene ontology: tool for the unification of biology. the gene ontology consortium. Nature Genetics 25(1), 25–29 (2000)
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., Kanehisa, M.: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research 27(1), 29–34 (1999)
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He, J. (2010). Improving Sequence Alignment Based Gene Functional Annotation with Natural Language Processing and Associative Clustering. In: Zhang, L., Lu, BL., Kwok, J. (eds) Advances in Neural Networks - ISNN 2010. ISNN 2010. Lecture Notes in Computer Science, vol 6064. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-13318-3_39
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DOI: https://doi.org/10.1007/978-3-642-13318-3_39
Publisher Name: Springer, Berlin, Heidelberg
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