Classification of genomic signals using dynamic time warping

BMC Bioinformatics

Volumn 14, Issue SUPPL10, 2013, Pages

  Skutkova, Helena ^a   Vitek, Martin ^a,b   Babula, Petr ^b   Kizek, Rene ^c   Provaznik, Ivo ^a,b  

^a BRNO UNIVERSITY OF TECHNOLOGY   (Czech Republic)

^b ST ANNE S UNIVERSITY HOSPITAL   (Czech Republic)

^c MENDEL UNIVERSITY IN BRNO   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION METHODS; DNA SEQUENCES ALIGNMENTS; DYNAMIC TIME WARPING; MULTIPLE SEQUENCE ALIGNMENTS; PHYLOGENETIC ANALYSIS; PHYLOGENETIC TREES; SIGNAL REPRESENTATIONS; SYMBOLIC REPRESENTATION;

BIOLOGY; CLUSTER ANALYSIS; DNA; DNA SEQUENCES;

GENES;

ACTIN;

ANIMAL; CHICKEN; CLASSIFICATION; EVOLUTION; GENETICS; GENOMICS; HEREDITY; HUMAN; MOLECULAR DYNAMICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROCEDURES; RHESUS MONKEY; SEQUENCE ALIGNMENT; SIGNAL TRANSDUCTION; TIME; ARTICLE; METHODOLOGY;

ACTINS; ANIMALS; BASE SEQUENCE; BIOLOGICAL EVOLUTION; CHICKENS; GENETIC PROCESSES; GENOMICS; HUMANS; MACACA MULATTA; MOLECULAR DYNAMICS SIMULATION; PHYLOGENY; SEQUENCE ALIGNMENT; SIGNAL TRANSDUCTION; TIME FACTORS;

EID: 84886837893     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-S10-S1     Document Type: Article

References (18)

1. Machado JAT, Costa AC, Quelhas MD. Wavelet analysis of human DNA. Genomics 2011, 98(3):155-163. 10.1016/j.ygeno.2011.05.010, 21672622.
2. Anastassiou D. Frequency-domain analysis of biomolecular sequences. Bioinformatics 2000, 16(12):1073-1081. 10.1093/bioinformatics/16.12.1073, 11159326.
3. Yau SST, Wang JS, Niknejad A, Lu C, Jin N, Ho YK. DNA sequence representation without degeneracy. Nucleic Acids Research 2003, 31(12):3078-3080. 10.1093/nar/gkg432, 162336, 12799435.
4. Cristea PD. Conversion of nucleotides sequences into genomic signals. Journal of Cellular and Molecular Medicine 2002, 6(2):279-303. 10.1111/j.1582-4934.2002.tb00196.x, 12169214.
5. Cristea PD. Large scale features in DNA genomic signals. Signal Processing 2003, 83(4):871-888.
6. Legrand B, Chang CS, Ong SH, Neo SY, Palanisamy N. Chromosome classification using dynamic time warping. Pattern Recognition Letters 2008, 29(3):215-222.
7. Huelsenbeck JP. Performance of phylogenetic methods in simulation. Systematic Biology 1995, 44(1):17-48.
8. Otu HH, Sayood K. A new sequence distance measure for phylogenetic tree construction. Bioinformatics 2003, 19(16):2122-2130. 10.1093/bioinformatics/btg295, 14594718.
9. Rosenberg MS. Multiple sequence alignment accuracy and evolutionary distance estimation. BMC Bioinformatics 2005, 6(278). 1318491, 16305750.
10. Skutkova H, Provaznik I, Kizek R. Influence of sample variance on the phylogenetic reconstruction of protein sequences. Proceedings of the 4th International Symposium on Applied Sciences in Biomedical and Communication Technologies; Barcelona, Spain 2011, 1-5. 2093741., http://dl.acm.org/citation.cfm?id=2093741
11. Oikonomou KG, Zachou K, Dalekos GN. Alpha-actinin: A multidisciplinary protein with important role in B-cell driven autoimmunity. Autoimmun Rev 2011, 10(7):389-396. 10.1016/j.autrev.2010.12.009, 21241830.
12. Sakoe H, Chiba S. Dynamic-programming algorithm optimization for spoken word recognition. Ieee Transactions on Acoustics Speech and Signal Processing 1978, 26(1):43-49.
13. Giorgino T. Computing and Visualizing Dynamic Time Warping Alignments in R: The dtw Package. Journal of Statistical Software 2009, 31(7):1-24., http://www.jstatsoft.org/v31/i07/paper
14. Skutkova H, Vitek M, Krizkova S, Kizek R, Provaznik I. Preprocessing and classification of electrophoresis gel images using dynamic time warping. Int J Electrochem Sci 2013, 8(2)., http://www.electrochemsci.org/papers/vol8/80201609.pdf
15. Burr T. Phylogenetic Trees in Bioinformatics. Curr Bioinform 2010, 5(1):40-52.
16. Jukes TH, Cantor CR. Evolution of Protein Molecules. 1969, Academy Press.
17. Hampl V, Pavlicek A, Flegr J. Construction and bootstrap analysis of DNA fingerprinting-based phylogenetic trees with the freeware program FreeTree: application to trichomonad parasites. International Journal of Systematic and Evolutionary Microbiology 2001, 51:731-735. 10.1099/00207713-51-3-731, 11411692.
18. Holmes S. Statistics for phylogenetic trees. Theoretical Population Biology 2003, 63(1):17-32. 10.1016/S0040-5809(02)00005-9, 12464492.