New Algorithm for Aligning Biological Data

  • Wajih RhalemEmail author
  • Mourad Raji
  • Ahmed Hammouch
  • Hassan Ghazal
  • Jamel El Mhamdi
Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 1076)


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.


Time series Signal alignment SHAPE data Logarithmic complexity SHAPEfinder 


  1. 1.
    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)Google Scholar
  2. 2.
    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)Google Scholar
  3. 3.
    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)Google Scholar
  4. 4.
    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)Google Scholar
  5. 5.
    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)Google Scholar
  6. 6.
    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)Google Scholar
  7. 7.
    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)Google Scholar
  8. 8.
    Itakura, F.: Minimum prediction residual principle applied to speech recognition. IEEE Trans. Acoust. Speech Signal Process ASSP 23, 52–72 (1975)Google Scholar
  9. 9.
    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)Google Scholar
  10. 10.
    Folgado, D., Barandas, M., Matias, R., Martins, R., Carvalho, M.: Time alignment measurement for time series. Patt. Recognit. 81, 268–279 (2018)Google Scholar
  11. 11.
    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)Google Scholar
  12. 12.
    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)Google Scholar
  13. 13.
    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)Google Scholar
  14. 14.
    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)Google Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2020

Authors and Affiliations

  • Wajih Rhalem
    • 1
    Email author
  • Mourad Raji
    • 1
  • Ahmed Hammouch
    • 2
  • Hassan Ghazal
    • 3
  • Jamel El Mhamdi
    • 1
  1. 1.LRGE LaboratoryENSET Mohammed V UniversityRabatMorocco
  2. 2.Direction of Scientific Research and InnovationMinistry of Higher EducationRabatMorocco
  3. 3.National Center for Scientific and Technical Research (CNRST)RabatMorocco

Personalised recommendations