Evolutionary ordering of the mitochondrion-encoded proteins

• Autorzy: Kozarzewski B.
• Języki publikacji: EN

Abstrakty

EN

The parsing of a symbolic sequence into a set of short substrings called words invented by the author is used for a new definition of the distance between sequences. No sequence alignment is necessary. The most frequent among spectra of multiprotein sequences are selected and considered as a reference spectrum of the sequences. The distance between the reference spectrum and protein sequences is considered as the estimation of the evolutionary distance of the protein. As an application, amino acid sequences of the several mitochondria-encoded proteins of mammal species are ordered according to their evolutionary distance. Statistical distribution of the distances between exhibits some structures related to the evolutionary rate in the past.

Słowa kluczowe

EN

symbolic sequence; parsing; distance

PL

ciąg symboliczny; analiza składniowa; odległość

• Wydawca: Wydawnictwo Politechniki Łódzkiej
• Czasopismo: Journal of Applied Computer Science
• Rocznik: 2016
• Tom: Vol. 24, nr 1
• Strony: 37--49
• Opis fizyczny: Bibliogr. 11 poz., wykr.

Twórcy

autor

Kozarzewski B.

• University of Information Technology and Management, Faculty of Applied Computer Science, H. Sucharskiego 2, 35-225 Rzeszow, Poland

Bibliografia

• [1] Kumar, S. and Filipski, A., Multiple sequence alignment: In pursuit of homologous DNA positions, Genome Research, Vol. 17, 2007, pp. 127–135.
• [2] Zuckerkandl, E. and Pauling, L., Molecular restoration studies of extinct forms of life, Acta Chemica Scandinavica, Vol. 17, 1963, pp. 9–16.
• [3] Schluter, D., Uncertainty in ancient phylogenies, Nature, Vol. 377, 1995, pp. 108–110.
• [4] Rosenberg, M., S., Multiple sequence alignment accuracy and evolutionary distance estimation, Bioinformatics, Vol. 6, 2005, pp. 278–288.
• [5] Williams, P., D., Pollock, D., D., Blackburne, B., P., and Goldstein, R., A., Assessing the accuracy of ancestral protein reconstruction methods, PLoS Comput. Biol., Vol. 2, 2006, pp. 598–605.
• [6] Kozarzewski, B., A method for nucleotide sequence analysis, Computational Methods in Science and Technology, Vol. 18, No. 2, 2012, pp. 5–10.
• [7] Vinga, P. and Almeida, J., Alignment-free sequence comparison - a review, Bioinformatics, Vol. 19, 2003, pp. 513–523.
• [8] Ke, D., G. and Tong, Q., Y., Easily adaptable complexity measure for finite time series, Phys. Rev., Vol. E77, 2008, pp. 513066215–23.
• [9] Nei, M., Xu, P., and Glazko, G., Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms, Proc. Nat. Acad. Sciences, Vol. 98, 2001, pp. 2497–2502.
• [10] Caswell, J., Mallick, S., Richter, D., Neubauer, J., Schirmer, C. end Gnerre, S., and Reich, D., Analysis of Chimpanzee History Based on Genome Sequence Alignments, PLoS Genetics, Vol. 4, No. 4, 2008.
• [11] Bromham, L. and Penny, D., The modern molecular clock, Nature Reviews, Genetics, Vol. 4, pp. 216–224.

Uwagi

Opracowanie ze środków MNiSW w ramach umowy 812/P-DUN/2016 na działalność upowszechniającą naukę.