IEEE/OSA/IAPR International Conference on Informatics, Electronics & Vision

Prediction of Protein Coding Regions of a DNA

Sequence through Spectral Analysis

S.Barman(Mandal) A.Mandal
Institute of Radiophysics and Electronics Institute of Radiophysics and Electronics
University of Calcutta University of Calcutta
92, A.P.C Road, Kolkata-700009, India 92, A.P.C Road, Kolkata-700009, India
E-mail: barman_s@email.com

S.Saha M.Roy
Institute of Radiophysics and Electronics The Calcutta Technical School
University of Calcutta Govt. of West Bengal,
92, A.P.C Road, Kolkata-700009, India Kolkata, India

Abstract- Accurate exon prediction in a genome is extremely
important for understanding of life processes. Researchers use
various techniques for detecting accurate location of exons. A
digital filter model has been proposed in this paper for the
prediction of exons in DNA sequence. The technique involves
conversion of DNA character string into a numerical sequence
using weak-strong bonding of nucleotides and filtering the
transformed sequence using Narrow Band Pass FIR filter whose
passband is centered at 2π/3. The filtered signal power of Narrow
band pass FIR filter is then used as a measure parameter for
both exons and introns. A plot of signal power versus nucleotide
location is used to distinguish exons from introns of a DNA
sequence. The simulation plots show very distinct peaks in exon
regions indicating its presence where as such peaks are absent in
intron regions. The design model is tested for several databases of
Homo sapiens Beta-globin chromosome which have been
downloaded from National Center for Biotechnology Information
(NCBI) homepage.
Index Terms- Genomics, Amino acids, Deoxyribonucleic Acid
(DNA), Power Spectral Density, Protein Coding Region, Digital
Filter.
sequence is always written from 5’ end to 3’ end which is
called polarity of DNA chain. Figure 1 illustrates the
organization of DNA in eukaryotic genes. Two types of
nitrogenous bases purine and pyrimidine are present in DNA.
‘A’ and ‘G ’are purine bases where as ‘C’ and ‘T’ are
pyrimidine bases. The DNA strands are held together mainly
by hydrogen bonds between bases. There are two hydrogen
bonds between ‘A’ and ‘T’ while three hydrogen bonds exist
between ‘C’ and ‘G’. Hence ‘C’ and ‘G’ bonds are stronger
than ‘A’ and ‘T’ bonds as depicted in Fig.2 and in Fig. 3.
DNA is usually divided into coding (exon) and non coding
(intron) regions. Only exons are responsible for protein
synthesis and introns are spliced off before manufacturing of
protein.
Gene prediction refers to detecting locations of protein –
coding regions (exon) of genes in a long DNA sequence which
is one of the most important step for understanding life
process. A challenging problem to the researchers is to
identify the exon location of a DNA sequence which help in
determining protein functions.

I. INTRODUCTION

The hereditary information needed to build and maintain a

living organism resides in its genome. The genome contains
genes which are made of DNA. DNA is a very large
biomolecule, made up of smaller units called nucleotides.
Genetic information is believed to be stored in the particular
order of four kinds of nucleotide bases, Adenine(A),
Thymine(T), Cytosine(C) and Guanine(G). Thus a DNA can
be represented as a string of character. There are two
complementary DNA chains twisted around one another in a
right handed double helix structure. The two strands of DNA
are always complementary to one another. Adenine (A) of one
strand always pairs with Thymine (T) of opposite strand while Fig 1. Organization of Genes in eukaryotes
Guanine (G) always pairs with Cytosine (C). DNA base

978-1-4673-1154-0/12/$31.00 ©2012 IEEE ICIEV 2012

 IEEE/OSA/IAPR International Conference on Informatics, Electronics & Vision
Digital Signal Processing (DSP) techniques offer a great
promise in analyzing genomic data because of its digital
nature.
Adenine (A)
H H
H N
N H
C O O C
H
N O N N
N O
Purine
2 Rings
Fig 2. Hydrogen bonds between neucleotides
A number of authors have devised algorithms for detection
of protein coding regions in genomic sequence by finding
regions exhibiting period-3 characteristic [1]. Vaidyanathan
and Yoon [2] applied an anti notch Infinite Impulse Response
(IIR) digital filter to the indicator sequences to detect the
period - 3 component. The Discrete Fourier Transform (DFT)
approach to find the 3 – periodicity regions in genomic
sequences has been used by various authors [3, 4, 5]. Tiwari
etal [6] presented an early study of application of DFT for
gene prediction. Epps etal [7] developed an integer period
DFT for biological sequence processing that had certain
advantages in detecting DNA periodicity. Roy etal [8]
introduced an algorithm called Positional Frequency
Distribution of Nucleotides (PFDN) which predicted exon
regions based on distribution of nucleotides in exons and
intron regions. Ramachandan etal [9, 10] used Electron-ion
interaction potential (EIIP) values for locating hot spots in
protein. In this technique, a Narrow Band Pass (NBP) digital
filter is used to select the characteristic frequency of interest.
Guanine (G) Cytosine (C)
H
H N
O N
H H
C
C O C C
N C N H N C
N O C N
Purine
N
H O
2 Rings
H
Fig 3. Triple Hydrogen Bond C Ξ G Signifies strong bond
The authors in this paper a cascade of Bandpass FIR and
Low pass IIR filter is used to measure the signal power both in
exon and intron regions of a DNA sequence. The filtering
technique gives prominent and satisfactory results for
prediction of exon region.
The paper is organized as follows: Section 2 presents
binary mapping technique, Section 3 elaborates details of
13
filtering technique, Section 4 presents the results obtained and
Section 5 gives the conclusion.
The following techniques have been tested for several
databases of Homo sapiens chromosomes.
Thymine (T)
II. DNA REPRESENTATION USING MAPPING
H H
O C
C
Signal processing analysis of Genomic sequences is hindered
by their representation as string of four letter characters A, T,
C H
C, G . Hence a mapping technique is required to convert the
C N sequence into numerals before applying DSP techniques.
Different researchers have adopted different mapping methods
O Pyrimidine
1 Ring
for this purpose. Here the authors have attempted a mapping
rule based on weak-strong hydrogen bonding for digitization.
As nucleotides ‘A’ and ‘T’ have two hydrogen bonds in their
molecular structure they have been treated as weak bond and
assigned value ‘-1’. Nucleotides ‘C’ and ‘G’ have three
hydrogen bonds so they are treated as strong and have been
assigned value ‘1’ of nucleotide data base .
For example a DNA sequence of length N:
x[n] = [A T G C C T T A G G A T] (1)
After mapping:
xsw[n] = [-1 -1 1 1 1 -1 -1 -1 1 1 -1 -1] (2)
The mapping technique based on weak and strong base is
better choice for numerically representing DNA sequence
compared to binary indicator method proposed by Voss [11]
because it not only generates single sequence but is also
biologically more meaningful as it represent physical property
of nucleotides. After this conversion DSP methods can be
applied effectively to extract the hidden features of DNA
sequences.
III. DIGITAL FILTERING TECHNIQUE
From DSP perspective, the prediction of exon regions using
digital filtering is achieved through spectral analysis of DNA
sequence by comparing the strength of the signal in coding and
non coding region along the length of a DNA sequence.
In our technique the mapped discrete signal is transformed
into another signal in frequency domain using Discrete Fourier
transform. Then it is passed through a narrowband Finite
H Impulse Response (FIR) bandpass filter with its passband
centered at the period – 3 frequency of 2π/3 which is used to
filter the transformed DNA sequence and is then squared. The
Pyrimidine
strength of the signal is used as the measure parameter of the
1 Ring period-3 property of coding region after passing the squared
signal again through an IIR lowpass filter. A very sharp peak is
observed in exon region which is absent in intron regions.
The DFT of the indicator sequence, obtained by the
mapping technique employed is given by
Xs[k] = ∑xs[n]e-j2πnk/n
Where
xs[n]=[-1 1 1 -1 1-1 -1 1 …………..],
DFT of xs[n] = Xs[k],
ICIEV 2012
 IEEE/OSA/IAPR International Conference on Informatics, Electronics & Vision

k= 0,1,2,…..N-1 For the IIR LP filter design the normalized cutoff

n= 0,1,2…...N-1
s= A, C, G, T
A MATLAB simulink environment has been created to
filter the DNA signal. The proposed exon prediction model,
amplitude response of FIR bandpass and IIR lowpass filter
have been shown in Fig. 4, Fig. 5 and Fig. 6 respectively.
frequency and order of filter have been chosen to be 0.24 and
10 respectively and the attenuation at cutoff frequencies is
fixed at 3 dB.
Figure 7 shows simulated output of our proposed model
both for exon and intron regions of DNA sequence. The
simulation results show very sharp peaks in exon regions
whereas such peaks are absent in intron regions.
The signal strength in coding region is found to be 10 times
more than the signal strength of non-coding regions. The sharp
peaks in exon regions show period-3 property present in
protein coding regions.

Accession No.: AF007546

EXON (Relative Position: 402-624 Length: 223)

Fig 4. Proposed model for exon prediction

Fig 5. FIR Band pass Filter response

INTRON (Relative Position: 625-1474 Length: 850)

Fig 6. IIR Low pass Filter response

IV. RESULTS AND DISCUSSION

The proposed model is tested for a set of Homo sapiens beta-

globin (HBB) genes downloaded from NCBI homepage. The
Accession numbers AF007546, AF083883, AF059180,
EF450778, AF527577, DQ074763, AY163866, DQ126271,
EU761578 and DQ157442 have been used to evaluate the
performance of the proposed model.
In this model, a FIR bandpass (BP) filter with Blackman
Window and IIR lowpass (LP) filter with Butterworth
approximation have been used by trial and error method.
For the FIR BP filter design approach the following
normalized passband edges have been chosen
wc1 = 0.6665 and wc2 = 0.6667
The minimum filter order = 100.
The attenuation at cutoff frequencies is fixed at 6 dB.

14 ICIEV 2012
 IEEE/OSA/IAPR International Conference on Informatics, Electronics & Vision
Accession No. AF059180
EXON (Relative Position:27-118
INTRON (Relative Position:119-248
Accession No. AF083883
EXON (Relative Position: 27-118
INTRON (Relative Position: 475-1321 Length: 850)
15
Accession No. EF450778
EXON (Relative Position: 565-787 Length: 223)
Length:92)
Length: 130) INTRON (Relative Position: 435-564 Length: 130)
Fig 7. Simulation results of proposed model
Length: 92) V. CONCLUSION
In this paper, a digital filter based model has been
proposed to predict exon regions of a DNA sequence. The
performance of the model is successfully tested for the several
Homo sapiens databases of HBB gene taken from public
genome data bases. The exon regions are distinguished from
intron regions of a DNA sequence through spectral analysis
based on well-defined peaks in the waveform. Simulation
results show the proposed model is efficient for the prediction
of exon region. For efficient digital processing of DNA signal
weak-strong bond based mapping is used in the present paper.
Application of EIIP based mapping may further enhance the
accuracy of the proposed model to predict exon regions of a
DNA sequence. Alternate types of filters such as notch filter,
multiband filter may also be investigated to improve the
accuracy of the prediction. Phase distortion and phase
response of the filters are eliminated for simplicity of analysis.
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