SAGA: A novel signal alignment method based on genetic algorithm

Information Sciences

Volumn 228, Issue , 2013, Pages 113-130

  Kaya, Hüseyin ^a   Gündüz Öǧüdücü, Şule ^a  

^a ISTANBUL TECHNICAL UNIVERSITY   (Turkey)

Author keywords

Genetic algorithm; Signal alignment; Time warping

Indexed keywords

ALIGNMENT ALGORITHMS; ALIGNMENT METHODS; EXTRACTING FEATURES; PAIRWISE ALIGNMENT; PEAK WIDTHS; RAW SIGNALS; REAL-WORLD DATASETS; TIME AXIS; TIME WARPING; WARPED SIGNALS; WARPING FUNCTION;

FEATURE EXTRACTION; GENETIC ALGORITHMS;

ALIGNMENT;

EID: 84873117425     PISSN: 00200255     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ins.2012.12.012     Document Type: Article

References (32)

1. K.M. Aberg, E. Alm, and R.J.O. Torgrip The correspondence problem for metabonomics datasets Analytical and Bioanalytical Chemistry 394 2009 151 162
2. L.M. Akella, T. Rejtar, C. Orazine, M. Hincapie, and W.S. Hancock CLUE-TIPS, clustering methods for pattern analysis of LC-MS data Journal of Proteome Research 8 2009 4732 4742
3. A. Auger Convergence results for the (1, λ)-SA-ES using the theory of φ-irreducible Markov chains Theoretical Computer Science 334 2005 35 69
4. R. Bellman Dynamic Programming 2003 Dover Publications Inc.
5. J. Bonfield, C. Rada, and R. Staden Automated detection of point mutations using fluorescent sequence trace subtraction Nucleic Acids Research 26 1998 3404 3409
6. D. Bylund, R. Danielsson, G. Malmquist, and K. Markides Chromatographic alignment by warping and dynamic programming as a pre-processing tool for PARAFAC modelling of liquid chromatography-mass spectrometry data Journal of Chromatography A 961 2002 237 244
7. M. Crowe SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms BMC Bioinformatics 6 2005
8. P.H.C. Eilers Parametric time warping Analytical Chemistry 76 2004 404 411
9. B. Ewing, L. Hillier, M. Wendl, and P. Green Base-calling of automated sequencer traces using Phred. I. Accuracy assessment Genome Research 8 1998 175 185
10. S. Kwong, C.W. Chau, and W.A. Halang Genetic algorithm for optimizing the nonlinear time alignment of automatic speech recognition systems IEEE Transactions on Industrial Electronics 43 1996 559 566
11. J. Listgarten, Analysis of Sibling Time Series Data: Alignment and Difference Detection, Ph.D. thesis, University of Toronto, 2007.
12. J. Listgarten, R.M. Neal, S.T. Roweis, and A. Emili Multiple alignment of continuous time series Advances in Neural Information Processing Systems 2005 MIT Press 817 824
13. G. Maletti, B. Ersbol, and K. Conradsen A combined alignment and registration scheme of lesions with psoriasis Information Sciences 175 2005 141 159
14. C. Manaster, W. Zheng, M. Teuber, S. Wachter, F. Doring, S. Schreiber, and J. Hampe InSNP: a tool for automated detection and visualization of SNPs and InDels Human Mutation 26 2005 11 19
15. R. Mott Trace alignment and some of its applications Bioinformatics 14 1998 92 97
16. D. Nickerson, V. Tobe, and S. Taylor PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing Nucleic Acids Research 25 1997 2745 2751
17. N.P.V. Nielsen, J.M. Carstensen, and J. Smedsgaard Aligning of single and multiple wavelength chromatographic profiles for chemometric data analysis using correlation optimised warping Journal of Chromatography A 805 1998 17 35
18. J.O. Ramsay Estimating smooth monotone functions Journal of the Royal Statistical Society Series B-Statistical Methodology 60 1998 365 375
19. J.O. Ramsay, and X.C. Li Curve registration Journal of the Royal Statistical Society Series B-Statistical Methodology 60 1998 351 363
20. C. Ratanamahatana, E. Keogh, Making time-series classification more accurate using learned constraints, in: Proceedings of the Fourth SIAM International Conference on Data Mining, 2004, pp. 11-22.
21. M.D. Robinson, D.P. De Souza, W.W. Keen, E.C. Saunders, M.J. McConville, T.P. Speed, and V.A. Likic A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments BMC Bioinformatics 8 2007
22. H. Sakoe, and S. Chiba Dynamic-programming algorithm optimization for spoken word recognition IEEE Transactions on Acoustics Speech and Signal Processing 26 1978 43 49
23. S. Salvadora, and P. Chan Toward accurate dynamic time warping in linear time and space Intelligent Data Analysis 11 2007 561 580
24. F. Sanger, S. Nicklen, and A. Coulson DNA sequencing with chain-terminating inhibitors Proceedings of the National Academy of Sciences of the United States of America 74 1977 5463 5467
25. A.A. Smith, Classification and Alignment of Gene-Expression Time-Series Data, Ph.D. thesis, University of Wisconsin - Madison, 2009.
26. A.A. Smith, A. Vollrath, C.A. Bradfield, and M. Craven Clustered alignments of gene-expression time series data Bioinformatics 25 2009 i119 i127
27. N.K.S. Thalange, P.J. Foster, M.S. Gill, D.A. Price, and P.E. Clayton Model of normal prepubertal growth Archives of Disease in Childhood 75 1996 427 431
28. G. Tomasi, F. van den Berg, and C. Andersson Correlation optimized warping and dynamic time warping as preprocessing methods for chromatographic data Journal of Chemometrics 18 2004 231 241
29. B. Walczak, and W. Wu Fuzzy warping of chromatograms Chemometrics and Intelligent Laboratory Systems 77 2005 173 180
30. D. Yu, X. Yu, Q. Hu, J. Liu, and A. Wu Dynamic time warping constraint learning for large margin nearest neighbor classification Information Sciences 181 2011 2787 2796
31. Y. Yuan, Y.P.P. Chen, S. Ni, A.G. Xu, L. Tang, M. Vingron, M. Somel, and P. Khaitovich Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series BMC Bioinformatics 12 2011
32. M. Zhou, and M. Wong A segment-wise time warping method for time scaling searching Information Sciences 173 2005 227 254