Accessible Requires Authentication Published by De Gruyter June 23, 2016

Search of latent periodicity in amino acid sequences by means of genetic algorithm and dynamic programming

Valentina Pugacheva, Alexander Korotkov and Eugene Korotkov

Abstract

The aim of this study was to show that amino acid sequences have a latent periodicity with insertions and deletions of amino acids in unknown positions of the analyzed sequence. Genetic algorithm, dynamic programming and random weight matrices were used to develop a new mathematical algorithm for latent periodicity search. A multiple alignment of periods was calculated with help of the direct optimization of the position-weight matrix without using pairwise alignments. The developed algorithm was applied to analyze amino acid sequences of a small number of proteins. This study showed the presence of latent periodicity with insertions and deletions in the amino acid sequences of such proteins, for which the presence of latent periodicity was not previously known. The origin of latent periodicity with insertions and deletions is discussed.

Acknowledgments

This work was supported by the grant 2014-04-00164 of the Russian Fund of Fundamental Research.

References

Afreixo, Vera, Paulo J. S. G. Ferreira and Dorabella Santos (2004): “Fourier analysis of symbolic data: a brief review,” Digit. Signal Process, 14, 523–530. Search in Google Scholar

Almirantis, Yannis, Peter Arndt, Wentian Li and Astero Provata (2014): “Editorial: complexity in genomes,” Comput. Biol. Chem., 53(Pt A), 1–4. Search in Google Scholar

Altschul, S. F., W. Gish, W. Miller, E. W. Myers and D. J. Lipman (1990): “Basic local alignment search tool,” J. Mol. Biol., 215, 403–410. Search in Google Scholar

Andrade, M. A, C. P. Ponting, T. J. Gibson and P. Bork (2000): “Homology-based method for identification of protein repeats using statistical significance estimates,” J. Mol. Biol., 298, 521–537. Search in Google Scholar

Bäck, Thomas (1996): Evolutionary algorithms in theory and practice: evolution strategies, evolutionary programming, genetic algorithms, Oxford, UK: Oxford University Press. Search in Google Scholar

Banzhaf, Wolfgang, Frank D. Francone, Robert E. Keller and Peter Nordin (1998): Genetic programming: an introduction: on the automatic evolution of computer programs and its applications. San Francisco, CA, USA: Morgan Kaufmann. Search in Google Scholar

Biegert, A. and J. Söding (2008): “De novo identification of highly diverged protein repeats by probabilistic consistency,” Bioinformatics, 24, 807–814. Search in Google Scholar

Björklund, Asa K., Diana Ekman and Arne Elofsson (2006): “Expansion of protein domain repeats,” PLoS Comput. Biol., 2:e114. Search in Google Scholar

Boeckmann, Brigitte, A. Bairoch, R. Apweiler, M. C. Blatter, A. Estreicher, E. Gasteiger, M. J. Martin, K. Michoud, C. O’Donovan, I. Phan, S. Pilbout and M. Schneider (2003): “The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003,” Nucleic Acids Res., 31, 365–370. Search in Google Scholar

Dahlstrand, J., L. B. Zimmerman, R. D. McKay and U. Lendahl (1992): “Characterization of the human nestin gene reveals a close evolutionary relationship to neurofilaments,” J. Cell Sci., 103(Pt 2), 589–597. Search in Google Scholar

De Grassi, Anna and Francesca D. Ciccarelli (2009): “Tandem repeats modify the structure of human genes hosted in segmental duplications,” Genome Biol., 10, R137. Search in Google Scholar

Di Domenico, Tomás, E. Potenza, I. Walsh, R. G. Parra, M. Giollo, G. Minervini, D. Piovesan, A. Ihsan, C. Ferrari, A. V. Kajava and S. C. Tosatto (2014): “RepeatsDB: a database of tandem repeat protein structures,” Nucleic Acids Res., 42(D1), D352–D357. Search in Google Scholar

Do Viet, Phuong, Daniel B. Roche and Andrey V. Kajava (2015): “TAPO: a combined method for the identification of tandem repeats in protein structures,” FEBS Lett., 589(19 Pt A), 2611–2619. Search in Google Scholar

Durbin, R., S. Eddy, A. Krogh and G. Mitchison (1998): Biological sequence analysis: probabilistic models of proteins and nucleic acids, Cambridge, UK: Cambridge University Press. Search in Google Scholar

Ekblom, Robert and Jochen B. W. Wolf (2014): “A field guide to whole-genome sequencing, assembly and annotation,” Evol. Appl., 7, 1026–1042. Search in Google Scholar

Elkins, Patricia A., Y. S. Ho, W. W. Smith,C. A. Janson, K. J. D’Alessio, M. S. McQueney, M. D. Cummings and A. M. Romanic (2002): “Structure of the C-terminally truncated human ProMMP9, a gelatin-binding matrix metalloproteinase,” Acta Crystallogr. D. Biol. Crystallogr., 58(Pt 7), 1182–1192. Search in Google Scholar

Enkhbayar, Purevjav, Kunio Hikichi, Mitsuru Osaki, Robert H. Kretsinger and Norio Matsushima (2006): “3(10)-Helices in proteins are parahelices,” Proteins, 64, 691–699. Search in Google Scholar

Espada, Rocío, R. G. Parra, M. J. Sippl, T. Mora, A. M. Walczak and D. U. Ferreiro (2015): “Repeat proteins challenge the concept of structural domains,” Biochem. Soc. Trans., 43, 844–849. Search in Google Scholar

Fábián, P., V. S. Chauhan and S. Pongor (1994): “Predicted conformation of poly(dehydroalanine): a preference for turns,” Biochim. Biophys. Acta, 1208, 89–93. Search in Google Scholar

Fogel, David B. (1998): Evolutionary computation: the fossil record, Hoboken, NJ, USA: Wiley-IEEE Press. Search in Google Scholar

Fogel, David B. (2010): Evolutionary computation toward a new philosophy of machine intelligence, Piscataway, NJ, USA: IEEE Press. Search in Google Scholar

Gondro, C. and B. P. Kinghorn (2007): “A simple genetic algorithm for multiple sequence alignment,” Genet. Mol. Res., 6, 964–982. Search in Google Scholar

Heger, Andreas and Liisa Holm (2000): “Rapid automatic detection and alignment of repeats in protein sequences,” Proteins Struct. Funct. Genet., 41, 224–237. Search in Google Scholar

Heringa, J. and P. Argos (1993): “A method to recognize distant repeats in protein sequences,” Proteins, 17, 391–41. Search in Google Scholar

Holste, Dirk, Ivo Grosse, Stephan Beirer, Patrick Schieg and Hanspeter Herzel (2003): “Repeats and correlations in human DNA sequences,” Phys. Rev. E. Stat. Nonlin. Soft Matter Phys., 67(6 Pt 1), 061913. Search in Google Scholar

Jernigan, Kristin K. and Seth R. Bordenstein (2015): “Tandem-repeat protein domains across the tree of life,” PeerJ., 3:e732. Search in Google Scholar

Jorda, Julien and Andrey V. Kajava (2009): “T-REKS: identification of tandem REpeats in sequences with a K-meanS based algorithm,” Bioinformatics, 25, 2632–2638. Search in Google Scholar

Jorda, Julien, Bin Xue, Vladimir N. Uversky and Andrey V. Kajava (2010): “Protein tandem repeats – the more perfect, the less structured,” FEBS J., 277, 2673–2682. Search in Google Scholar

Kajava, Andrey V. (2012): “Tandem repeats in proteins: from sequence to structure,” J. Struct. Biol., 179, 279–288. Search in Google Scholar

Korotkov, E. V., M. A. Korotkova and N. A. Kudryashov (2003): “Information decomposition method to analyze symbolical sequences,” Phys. Lett. Sect. A Gen. At. Solid State Phys., 312, 198–210. Search in Google Scholar

Korotkov, E. V., M. A. Korotkova and N. A. Kudryashov (2003): “The informational concept of searching for periodicity in symbol sequences,” Mol. Biol. (Mosk)., 37, 436–451. Search in Google Scholar

Kravatskaya, G. I., Y. V. Kravatsky, V. R. Chechetkin and V. G. Tumanyan (2011): “Coexistence of different base periodicities in prokaryotic genomes as related to DNA curvature, supercoiling, and transcription,” Genomics, 98, 223–231. Search in Google Scholar

Kumar, Lokesh, Matthias Futschik and Hanspeter Herzel (2006): “DNA motifs and sequence periodicities,” In Silico Biol., 6, 71–78. Search in Google Scholar

Lee, M. S., G. P. Gippert, K. V Soman, D. A. Case and P. E. Wright (1989): “Three-dimensional solution structure of a single zinc finger DNA-binding domain,” Science, 245, 635–637. Search in Google Scholar

Lobzin, Vasilii V. and Vladimir R. Chechetkin (2000): “Order and correlations in genomic DNA sequences. the spectral approach,” Uspekhi Fiz. Nauk, 170, 57. Search in Google Scholar

Marcotte, E. M., M. Pellegrini, T. O. Yeates and D. Eisenberg (1999): “A census of protein repeats,” J. Mol. Biol., 293, 151–160. Search in Google Scholar

Mason, Jody M. and Katja M. Arndt (2004): “Coiled coil domains: stability, specificity, and biological implications,” Chembiochem, 5, 170–176. Search in Google Scholar

Meng, Tao, Ahmed T. Soliman, Mei-Ling Shyu, Yimin Yang, Shu-Ching Chen, S. S. Iyengar, John S. Yordy and Puneeth Iyengar (2013): “Wavelet analysis in current cancer genome research: a survey,” IEEE/ACM Trans. Comput. Biol. Bioinform., 10, 1442–1459. Search in Google Scholar

Mitchell, Melanie (1998): “An introduction to genetic algorithms,”. Search in Google Scholar

Morita, Tomotake, Naotaka Tanaka, Akira Hosomi, Yuko Giga-Hama and Kaoru Takegawa (2006): “An alpha-amylase homologue, aah3, encodes a GPI-anchored membrane protein required for cell wall integrity and morphogenesis in Schizosaccharomyces pombe,” Biosci. Biotechnol. Biochem., 70, 1454–1463. Search in Google Scholar

Mott, R. (1999): “Local sequence alignments with monotonic gap penalties,” Bioinformatics, 15, 455–462. Search in Google Scholar

Newman, Aaron M. and James B. Cooper (2007): “XSTREAM: a practical algorithm for identification and architecture modeling of tandem repeats in protein sequences,” BMC Bioinformatics, 8, 382. Search in Google Scholar

Palidwor, Gareth A., Sergey Shcherbinin, Matthew R. Huska, Tamas Rasko, Ulrich Stelzl, Anup Arumughan, Raphaele Foulle, Pablo Porras, Luis Sanchez-Pulido, Erich E. Wanker and Miguel A. Andrade-Navarro (2009): “Detection of alpha-rod protein repeats using a neural network and application to huntingtin,” PLoS Comput. Biol., 5, e1000304. Search in Google Scholar

Parra, R. Gonzalo, Rocío Espada, Ignacio E. Sánchez, Manfred J. Sippl and Diego U. Ferreiro (2013): “Detecting repetitions and periodicities in proteins by tiling the structural space,” J. Phys. Chem. B, 117, 12887–12897. Search in Google Scholar

Pellegrini, Marco (2015): “Tandem repeats in proteins: prediction algorithms and biological role,” Front. Bioeng. Biotechnol., 3, 143. Search in Google Scholar

Pellegrini, Marco, Maria Elena Renda and Alessio Vecchio (2012): “Ab initio detection of fuzzy amino acid tandem repeats in protein sequences,” BMC Bioinformatics, 13, S8. Search in Google Scholar

Polyanovsky, Valery O., Mikhail A. Roytberg and Vladimir G. Tumanyan (2011): “Comparative analysis of the quality of a global algorithm and a local algorithm for alignment of two sequences,” Algorithms Mol. Biol., 6, 25. Search in Google Scholar

Polyansky, Anton A., Anton O. Chugunov, Alexander A. Vassilevski, Eugene V Grishin and Roman G. Efremov (2012): “Recent advances in computational modeling of α-helical membrane-active peptides,” Curr. Protein Pept. Sci., 13, 644–657. Search in Google Scholar

Radcliffe, Nicholas J. (1991): “Equivalence class analysis of genetic algorithms,” Complex Syst., 5, 183–205. Search in Google Scholar

Richard, François D. and Andrey V. Kajava (2015): “In search of the boundary between repetitive and non-repetitive protein sequences,” Biochem. Soc. Trans., 43, 807–811. Search in Google Scholar

Rubinson, Emily H. and Brandt F. Eichman (2012): “Nucleic acid recognition by tandem helical repeats,” Curr. Opin. Struct. Biol., 22, 101–109. Search in Google Scholar

Sawaya, Michael R., W. M. Wojtowicz, I. Andre, B. Qian, W. Wu, D. Baker, D. Eisenberg and S. L. Zipursky (2008): “A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoforms,” Cell 134, 1007–1018. Search in Google Scholar

Shelenkov, Andrew, Konstantin Skryabin and Eugene Korotkov (2006): “Search and classification of potential minisatellite sequences from bacterial genomes,” DNA Res., 13, 89–102. Search in Google Scholar

Sippl, Manfred J. and Markus Wiederstein (2012): “Detection of spatial correlations in protein structures and molecular complexes,” Structure, 20, 718–728. Search in Google Scholar

Smith, T. F. and M. S. Waterman (1981): “Identification of common molecular subsequences,” J. Mol. Biol., 147, 195–197. Search in Google Scholar

Söding, Johannes, Michael Remmert and Andreas Biegert (2006): “HHrep: De novo protein repeat detection and the origin of TIM barrels,” Nucleic Acids Res., 34(Web Server issue), W137–W142. Search in Google Scholar

Sosa, Daniela, Pedro Miramontes, Wentian Li, Víctor Mireles, Juan R. Bobadilla and Marco V. José (2013): “Periodic distribution of a putative nucleosome positioning motif in human, nonhuman primates, and archaea: mutual information analysis,” Int. J. Genomics, 2013, 963956. Search in Google Scholar

de Sousa Vieira, M. (1999): “Statistics of DNA sequences: a low-frequency analysis,” Phys. Rev. E. Stat. Phys. Plasmas. Fluids. Relat. Interdiscip. Topics, 60(5 Pt B), 5932–5937. Search in Google Scholar

Spears, William M. and Kenneth D. De Jong (1991): “On the virtues of parameterized uniform crossover,” Proc. Fourth Int. Conf. Genet. Algorithms, Morgan Kaufmann Publ. Inc. San Fr. CA, USA 230–236. Search in Google Scholar

Suvorova, Yulia M., Maria A. Korotkova and Eugene V. Korotkov (2014): “Comparative analysis of periodicity search methods in DNA sequences,” Comput. Biol. Chem., 53(Pt A), 43–48. Search in Google Scholar

Sywerda, Gilbert (1989): “Uniform crossover in genetic algorithms,” Proc. Third Int. Conf. Genet. Algorithms, Morgan Kaufmann Publ. Inc. San Fr. CA, USA ©1989 2–9. Search in Google Scholar

Szklarczyk, Radek and Jaap Heringa (2004): “Tracking repeats using significance and transitivity,” Bioinformatics, 20(Suppl 1), i311–i317. Search in Google Scholar

Tiwari, S., S. Ramachandran, A. Bhattacharya, S. Bhattacharya and R. Ramaswamy (1997): “Prediction of probable genes by fourier analysis of genomic sequences,” Comput. Appl. Biosci. CABIOS, 13, 263–270. Search in Google Scholar

Turutina, Vera P., Andrew A. Laskin, Nikolay A. Kudryashov, Konstantin G. Skryabin and Eugene V. Korotkov (2006): “Identification of amino acid latent periodicity within 94 protein families,” J. Comput. Biol., 13, 946–964. Search in Google Scholar

Wolfner, Mariana F., H. A. Harada, M. J. Bertram, T. J. Stelick, K. W. Kraus, J. M. Kalb, Y. O. Lung, D. M. Neubaum, M. Park and U. Tram (1997): “New genes for male accessory gland proteins in Drosophila melanogaster,” Insect Biochem. Mol. Biol., 27, 825–834. Search in Google Scholar

Yang, Ruifeng, S. Bartle, R. Otto, A. Stassinopoulos, M. Rogers, L. Plamann and P. Hartzell (2004): “AglZ Is a filament-forming coiled-coil protein required for adventurous gliding motility of Myxococcus xanthus,” J. Bacteriol., 186, 6168–6178. Search in Google Scholar

Published Online: 2016-6-23
Published in Print: 2016-10-1

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