Short exon detection in DNA sequences based on multifeature spectral analysis

Eurasip Journal on Advances in Signal Processing

Volumn 2011, Issue , 2011, Pages

  Song, Nancy Yu ^a   Yan, Hong ^a  

^a CITY UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

AR MODELS; AUTO REGRESSIVE MODELS; DETECTION ALGORITHM; DIFFERENT SIZES; DNA BENDING; FEATURE-BASED METHOD; FREQUENCY COMPONENTS; HUMAN GENOMES; LINEAR PREDICTION; LINEAR PREDICTION COEFFICIENTS; MOVING WINDOW; NON-STATIONARITIES; SPECTRAL ANALYSIS;

DNA; NUCLEIC ACIDS; SPECTRUM ANALYSIS;

DNA SEQUENCES;

EID: 79251631964     PISSN: 16876172     EISSN: 16876180     Source Type: Journal    
DOI: 10.1155/2011/780794     Document Type: Article

References (27)

1. Watson J. D., Baker T. A., Bell S. P., RNA splicing Molecular Biology of the Gene 2008 6th chapter 13 Cold Spring Harbor, NY, USA Cold Spring Harbor Laboratory Press
2. Math C., Sagot M.-F., Schiex T., Rouz P., Current methods of gene prediction, their strengths and weaknesses Nucleic Acids Research 2002 30 19 4103 4117
3. Hawkins J. D., A survey on intron and exon lengths Nucleic Acids Research 1988 16 21 9893 9908
4. Fickett J. W., Recognition of protein coding regions in DNA sequences Nucleic Acids Research 1982 10 17 5303 5318
5. Xie X., Wu S., Lam K.-M., Yan H., PromoterExplorer: an effective promoter identification method based on the AdaBoost algorithm Bioinformatics 2006 22 22 2722 2728
6. Wu S., Xie X., Liew A. W.-C., Yan H., Eukaryotic promoter prediction based on relative entropy and positional information Physical Review E 2007 75 4 7
7. Durbin R., Eddy S., Krogh A., Mitchison G., Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids 1998 Cambridge, UK Cambridge University Press
8. Lorenzo-Ginori J. V., Rodrguez-Fuentes A., balo R. G., Rodrguez R. S., Digital signal processing in the analysis of genomic sequences Current Bioinformatics 2009 4 1 28 40
9. Tiwari S., Ramachandran S., Bhattacharya A., Bhattacharya S., Ramaswamy R., Prediction of probable genes by Fourier analysis of genomic sequences Computer Applications in the Biosciences 1997 13 3 263 270
10. Akhtar M., Ambikairajah E., Epps J., Optimizing period-3 methods for eukaryotic gene prediction Proceedings of the IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP '08) 2008 621 624
11. Vaidyanathan P. P., Yoon B.-J., Gene and exon prediction using allpass-based filters Proceedings of the IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS '02) October 2002 Raleigh, NC, USA
12. Romn-Roldn R., Bernaola-Galvn P., Oliver J. L., Sequence compositional complexity of DNA through an entropic segmentation method Physical Review Letters 1998 80 6 1344 1347
13. Nicorici D., Astola J., Segmentation of DNA into coding and noncoding regions based on recursive entropic segmentation and stop-codon statistics EURASIP Journal on Applied Signal Processing 2004 2004 1 81 91
14. Chakravarthy N., Spanias A., Iasemidis L. D., Tsakalis K., Autoregressive modeling and feature analysis of DNA sequences EURASIP Journal on Applied Signal Processing 2004 2004 1 13 28
15. Yan H., Pham T. D., Spectral estimation techniques for DNA sequence and microarray data analysis Current Bioinformatics 2007 2 2 145 156 (Pubitemid 46813408)
16. Choong M. K., Yan H., Multi-scale parametric spectral analysis for exon detection in DNA sequences based on forward-backward linear prediction and singular value decomposition of the double-base curves Bioinformation 2008 2 7 273 278
17. Jiang R., Yan H., Studies of spectral properties of short genes using the wavelet subspace Hilbert-Huang transform (WSHHT) Physica A 2008 387 16-17 4223 4247
18. George T. P., Thomas T., Discrete wavelet transform de-noising in eukaryotic gene splicing BMC Bioinformatics 2010 11 supplement 1, article S50
19. Wu Y., Liew A. W.-C., Yan H., Yang M., DB-Curve: a novel 2D method of DNA sequence visualization and representation Chemical Physics Letters 2003 367 1-2 170 176
20. Sivolob A. V., Khrapunov S. N., Translational positioning of nucleosomes on DNA: the role of sequence-dependent isotropic DNA bending stiffness Journal of Molecular Biology 1995 247 5 918 931
21. Florquin K., Saeys Y., Degroeve S., Rouz P., Van de Peer Y., Large-scale structural analysis of the core promoter in mammalian and plant genomes Nucleic Acids Research 2005 33 13 4255 4264
22. Breslauer K. J., Frank R., Blocker H., Marky L. A., Predicting DNA duplex stability from the base sequence Proceedings of the National Academy of Sciences of the United States of America 1986 83 11 3746 3750
23. Sugimoto N., Nakano S.-I., Yoneyama M., Honda K.-I., Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes Nucleic Acids Research 1996 24 22 4501 4505
24. El Hassan M. A., Calladine C. R., Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA Journal of Molecular Biology 1996 259 1 95 103
25. Yiou P., Sornette D., Ghil M., Data-adaptive wavelets and multi-scale singular-spectrum analysis Physica D 2000 142 3-4 254 290
26. Lang S. W., McClellan J. H., Frequency estimation with maximum entropy spectral estimator IEEE Transactions on Acoustics, Speech, and Signal Processing 1980 28 6 716 724
27. Youden W. J., Index for rating diagnostic tests Cancer 1950 3 1 32 35