Abstract
The change in data processing conditions obtained from biological experiments, in particular, SHAPE (Selective 2′-Hydroxyl Acylation analyzed by the Extension Primer) technique, results in the time shift of the data which are in the form of signals. In this study, a SHAPE data alignment algorithm is proposed using a new pattern recognition approach based on the discrete-to-continuous transition of entities. The advantage of our algorithm lies in the ability to process the information concerned with a logarithmic complexity, therefore, powerful results have been obtained.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Wilkinson, K.A., Merino, E.J., Weeks, K.M.: Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat. Protoc. 1, 1610–1616 (2006)
Vasa, S.M., Guex, N., Wilkinson, K.A., Weeks, K.M., Giddings, M.C.: ShapeFinder: a software system for highthroughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis. RNA 14, 1979–1990 (2008)
Raji, M., Cossé-Barbi, A.: Shape recognition and chirality measure: reestablishing the link between similarity and dissimilarity in discrete space. Chemom. Intell. Lab. Syst. 47, 219–225 (1999)
Aqili, N., Raji, M., Hammouch, A.: PPM translation, rotation and scale in D-dimensional space by the discrete to continuous approach. Int. Rev. Comput. Softw. IRECOS 11, 270–276 (2016)
Aqili, N., Maazouzi, A., Raji, M., Jilbab, A., Chaouki, S., Hammouch, A.: Fingerprint matching algorithm based on discrete to continuous approach. In: International Conference on Electrical and Information Technologies (ICEIT), pp. 414–417 (2016)
Aqili, N., Maazouzi, A., Raji, M., Jilbab, A., Chaouki, S., Hammouch, A.: On-line signature verification using point pattern matching algorithm. In: 2016 International Conference on Electrical and Information Technologies (ICEIT), pp. 410–413 (2016)
Maazouzi, A.-E., Aqili, N., Raji, M., Hammouch, A.: A speaker recognition system using power spectrum density and similarity measurements. In: Third World Conference Complex Systems (WCCS), pp. 1–5 (2015)
Itakura, F.: Minimum prediction residual principle applied to speech recognition. IEEE Trans. Acoust. Speech Signal Process ASSP 23, 52–72 (1975)
Kruskall, J.B., Liberman, M.: The symmetric time warping algorithm: from continuous to discrete. In: Time Warps, String Edits and Macromolecules: The Theory and Practice of String Comparison. Addison-Wesley (1983)
Folgado, D., Barandas, M., Matias, R., Martins, R., Carvalho, M.: Time alignment measurement for time series. Patt. Recognit. 81, 268–279 (2018)
Karabiber, F.: An automated signal alignment algorithm based on dynamic time warping for capillary electrophoresis data. Turk. J. Elec. Eng. Comp. Sci. 21, 851–863 (2013)
Gong, F., Liang, Y.Z., Fung, Y.S., Chau, F.T.: Correction of retention time shifts for chromatographic fingerprints of herbal medicines. J. Chromatogr. A, 1029, 173–83 (2004)
Tomasi, G., Van Den Berg, F., Andersson, C.: Correlation optimized warping and dynamic time warping as preprocessing methods for chromatographic data. J. Chemom. 18, 231–241 (2004)
Robinson, M.D., De Souza, D.P., Keen, W.W., Saunders, E.C., McConville, M.J., Speed, T.P., Likić, V.A.: A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments. BMC Bioinf. 8, 419 (2007)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Nature Singapore Pte Ltd.
About this paper
Cite this paper
Rhalem, W., Raji, M., Hammouch, A., Ghazal, H., El Mhamdi, J. (2020). New Algorithm for Aligning Biological Data. In: Bhateja, V., Satapathy, S., Satori, H. (eds) Embedded Systems and Artificial Intelligence. Advances in Intelligent Systems and Computing, vol 1076. Springer, Singapore. https://doi.org/10.1007/978-981-15-0947-6_68
Download citation
DOI: https://doi.org/10.1007/978-981-15-0947-6_68
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-15-0946-9
Online ISBN: 978-981-15-0947-6
eBook Packages: Intelligent Technologies and RoboticsIntelligent Technologies and Robotics (R0)