9.1 9.1 Introduction
Analysis of the DNA sequences of genes is important and necessary in the study of genetics, yet we still can not comprehend the whole meanings of DNA sequences. Many methods can be applied to their analysis, and the artificial neural network is one of the most frequent methods used to obtain the characteristic features of DNA sequences. Here we show how, though trial application, artificial neural networks acquire the features of splicing sites of DNA sequences.
When a protein is produced from a DNA chain, the sequence of the DNA is transcribed to the messenger RNA (mRNA). Then transfer RNA (tRNA) binds to the codons of the mRNA. Finally, the amino acids are polymerized to the protein. Not all the codons in the corresponding portion of DNA sequence are always translated to amino acids, however. After transcription to premature mRNA, the splicing process removes the noncoding sequences, called introns, and splices together with the remaining parts of premature mRNA,...
References
R. Breathnach and P. Chambon. Organization and expression of eucaryotic split genes coding for proteins. Annu. Rev. Biochem. 50: 349–383, 1981.
K. L. Denninghoff and R. W. Gatterdam. On the undecidability of splincing systems. Intern. J. Computer Math. 27: 133–145, 1989.
R. Carhart, J. Moore and A. Engelberg. Strategene, an expert assistant for genetic engineering research. Proceedings of the Third Annual Artificial Intelligence and Advanced Computer Technology Conference, 166–173, 1987.
K. Culik and T. Harju. Splicing semigroups of dominoes and DNA. Discrete Appl. Math. 31: 261–267, 1991.
A. Lapedes, C. Barnes, C. Burks, R. Farber and K. Sirotkin. SFI Studies in the Sciences of Complexity. Computer and DNA 7: 157–182, 1989.
E. C. Uberbacher and R. J. Mural. Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach. Proc. Natl. Acad. Sci. USA 88: 11261–11265, 1991.
H. Furutani, K. Yamamoto, Y. Kitazoe and H. Ogura. Analysis of thalassemia betaglobin gene by neural network: prediction of abnormal splice. MEDINFO 89. Preceeding of the Sixth Conference on Medical Informatics, pp. 96–100, 1989.
H. Ogura, H. Agata, M. Xie, T. Odaka and H. Furutani. A study of learning splice sites of DNA sequence by neural networks. Comput. Biol. Med. 27: 67–75, 1997.
T. Odaka, H. Agata, H. Furutani and H. Ogura. A general purpose neural network simulator system for medical data processing. J. Med. Sys. 18: 305–314, 1994.
F. Giannelli et al. Haemophilxia b: database of point mutations and short additions and deletions-second edition. Nucleic Acids Res. 19: 2193–2219, 1991.
J. D. Hirst and M. J. E. Sternberg. Prediction of structural and functional features of protein and nucleic acid sequences by artificial neural networks. Biochemistry 31: 7211–7218, 1992.
M. E. Mulligan and W. R. McClure. Analysis of the occurence of promoter-sites in DNA. Nucleic Acids Res. 14: 109–126, 1986.
M. C. O’Neill. Training back-propagation neural networks to define and detect DNA-binding sites. Nucleic Acids Res. 19: 313–318, 1991.
M. C. O’Neill. Escherichia coli promoters: neural networks develop distinct descriptions in learning to search for promoters of different spacing classes. Nucleic Acids Res. 20: 3471–3477, 1992.
I. Mahadevan and I. Ghosh. Analysis of E. coli promoter structures using neural networks. Nucleic Acids Res. 22: 2158–2165, 1994.
N. I. Larsen, J. Engelbrecht and S. Brunak. Analysis of eukaryotic promoter sequences reveals a systematically occurring CT-signal. Nucleic Acids Res. 23: 1223–1230, 1995.
P. Bucher. The Eukaryotic Promoter Database EPD EMBL Nucleotide Sequence Data Library, 1992.
N. Qian and T. J. Sejnowski. Predicting the secondary structure of globular proteins using neural network models. J. Molec. Biol. 202: 865–884, 1988.
L. H. Holley and M. Karplus. Protein secondary structure prediction with a neural network. Proc. Nat. Acad. Sci. USA 86: 768–774, 1989.
J. M. Chandonia and M. Karplus. Neural networks for secondary structure and structural class predictions. Protein Sci. 4: 275–285, 1995.
J. M. Chandonia and M. Karplus. The importance of larger data sets for protein secondary structure prediction with neural networks. Protein Sci. 5: 768–774, 1996.
B. Rost and C. Sander. Improved prediction of protein secondary structure by use of sequence profiles and neural networks. Proc. Natl. Acad. Sci. USA 90: 7558–7562, 1993.
Editor information
Rights and permissions
Copyright information
© 2003 Kluwer Academic Publishers
About this entry
Cite this entry
Leondes, C.T. (2003). An Application of Artificial Neural Networks to DNA Sequence Analysis. In: Leondes, C.T. (eds) Computational Methods in Biophysics, Biomaterials, Biotechnology and Medical Systems. Springer, Boston, MA. https://doi.org/10.1007/0-306-48329-7_9
Download citation
DOI: https://doi.org/10.1007/0-306-48329-7_9
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4020-7110-2
Online ISBN: 978-0-306-48329-5
eBook Packages: Springer Book Archive