Interpretive time-frequency analysis of genomic sequences

Hamed Hassani Saadi, Reza Sameni, Amin Zollanvari

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Background: Time-Frequency (TF) analysis has been extensively used for the analysis of non-stationary numeric signals in the past decade. At the same time, recent studies have statistically confirmed the non-stationarity of genomic non-numeric sequences and suggested the use of non-stationary analysis for these sequences. The conventional approach to analyze non-numeric genomic sequences using techniques specific to numerical data is to convert non-numerical data into numerical values in some way and then apply time or transform domain signal processing algorithms. Nevertheless, this approach raises questions regarding the relative magnitudes under numeric transforms, which can potentially lead to spurious patterns or misinterpretation of results. Results: In this paper, using the notion of interpretive signal processing (ISP) and by redefining correlation functions for non-numeric sequences, a general class of TF transforms are extended and applied to non-numerical genomic sequences. The technique has been successfully evaluated on synthetic and real DNA sequences. Conclusion: The proposed framework is fairly generic and is believed to be useful for extracting quantitative and visual information regarding local and global periodicity, symmetry, (non-) stationarity and spectral color of genomic sequences. The notion of interpretive time-frequency analysis introduced in this work can be considered as the first step towards the development of a rigorous mathematical construct for genomic signal processing.

Original languageEnglish
Article number154
JournalBMC Bioinformatics
Volume18
DOIs
Publication statusPublished - Mar 22 2017

Fingerprint

Time-frequency Analysis
Sequence Analysis
Genomics
Signal processing
Signal Processing
Time and motion study
Nonstationarity
DNA sequences
Transform
Numerics
Periodicity
Color
DNA Sequence
Convert
Correlation Function
Symmetry

Keywords

  • Genomic signal processing
  • Interpretive signal processing
  • Time-frequency analysis

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

Interpretive time-frequency analysis of genomic sequences. / Hassani Saadi, Hamed; Sameni, Reza; Zollanvari, Amin.

In: BMC Bioinformatics, Vol. 18, 154, 22.03.2017.

Research output: Contribution to journalArticle

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