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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Notes
- 1.
Auxin transport protein (BIG).
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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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