Abstract
The great increase in the amount of sequenced DNA has created a problem: the storage of the sequences. As such, data compression techniques, designed specifically to compress genetic information, is an important area of research and development. Likewise, the ability to search similar DNA sequences in relation to a larger sequence, such as a chromosome, has a really important role in the study of organisms and the possible connection between different species. This paper proposes NET-ASAR, a tool for DNA sequence search, based on data compression, or, specifically, finite-context models, by obtaining a measure of similarity between a reference and a target. The method uses an approach based on finite-context models for the creation of a statistical model of the reference sequence and obtaining the estimated number of bits necessary for the encoding of the target sequence, using the reference model. NET-ASAR is freely available, under license GPLv3, at https://github.com/manuelgaspar/NET-ASAR.
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Auxin transport protein (BIG).
References
Sanger, F., et al.: DNA sequencing with chain-terminating inhibitors. PNAS 74(12), 5463–5467 (1977)
Tomkins, J.: How genomes are sequenced and why it matters: implications for studies in comparative genomics of humans and chimpanzees. Answers Res. J. 4, 81–88 (2011)
Chen, X., et al.: DNACompress: fast and effective DNA sequence compression. Bioinformatics 18(12), 1696–1698 (2002)
Pinho, A.J., et al.: On the representability of complete genomes by multiple competing finite-context (Markov) models. PLoS ONE 6(6), e21588 (2011)
Cao, M.D., et al.: A simple statistical algorithm for biological sequence compression. In: Data Compression Conference, DCC 2007, pp. 43–52. IEEE (2007)
Christley, S., et al.: Human genomes as email attachments. Bioinformatics 25(2), 274–275 (2008)
Wang, C., Zhang, D.: A novel compression tool for efficient storage of genome resequencing data. Nucleic Acids Res. 39(7), e45 (2011)
Deorowicz, S., et al.: GDC 2: Compression of large collections of genomes. Sci. Rep. 5, 11565 (2015)
Altschul, S.F., et al.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17), 3389–3402 (1997)
Thompson, J.D., et al.: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22(22), 4673–4680 (1994)
Edgar, R.C.: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5), 1792–1797 (2004)
Darling, A.E., et al.: progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5(6), e11147 (2010)
Vialle, R.A., et al.: RAFTS3: Rapid Alignment-Free Tool for Sequence Similarity Search. bioRxiv 055269 (2016)
Zielezinski, A., et al.: Alignment-free sequence comparison: benefits, applications, and tools. Genome Biol. 18(1), 186 (2017)
Pinho, A.J., et al.: A three-state model for DNA protein-coding regions. IEEE Trans. Biomed. Eng. 53(11), 2148–2155 (2006)
Trifonov, E.N., Sussman, J.L.: The pitch of chromatin DNA is reflected in its nucleotide sequence. PNAS 77(7), 3816–3820 (1980)
Salomon, D.: Data Compression - The Complete Reference, 3rd edn. Springer Science & Business Media, London (2004)
Bell, T.C., et al.: Text Compression. Prentice Hall, Englewood Cliffs (1990)
Tatusova, T.A., Madden, T.L.: BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett. 174(2), 247–250 (1999)
Altschul, S.F., et al.: Basic local alignment search tool. J. Mol. Biol. 215(3), 403–410 (1990)
Pratas, D., et al.: Visualization of distinct DNA regions of the modern human relatively to a neanderthal genome. In: Iberian Conference on Pattern Recognition and Image Analysis, pp. 235–242. Springer (2017)
Pratas, D., et al.: Detection and visualisation of regions of human DNA not present in other primates. In: Proceedings of the 21st Portuguese Conference on Pattern Recognition, RecPad (2015)
Prüfer, K., et al.: The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505(7481), 43–49 (2014)
Meyer, M., et al.: A high-coverage genome sequence from an archaic Denisovan individual. Science 338(6104), 222–226 (2012)
Gaspar, M.: Automatic system for approximate and noncontiguous DNA sequences search. Master’s thesis, Universidade de Aveiro (2017)
Acknowledgments
This work was partially funded by National Funds through the FCT - Foundation for Science and Technology (UID/CEC/00127/2013, PTDC/EEI-SII/6608/2014).
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Gaspar, M., Pratas, D., Pinho, A.J. (2019). NET-ASAR: A Tool for DNA Sequence Search Based on Data Compression. In: Fdez-Riverola, F., Mohamad, M., Rocha, M., De Paz, J., González, P. (eds) Practical Applications of Computational Biology and Bioinformatics, 12th International Conference. PACBB2018 2018. Advances in Intelligent Systems and Computing, vol 803. Springer, Cham. https://doi.org/10.1007/978-3-319-98702-6_14
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