1. International Journal of Electronics and Communication Engineering & Technology (IJECET), ISSN 0976 –
INTERNATIONAL JOURNAL OF ELECTRONICS AND
6464(Print), ISSN 0976 – 6472(Online), Volume 5, Issue 2, February (2014), pp. 30-35 © IAEME
COMMUNICATION ENGINEERING & TECHNOLOGY (IJECET)
ISSN 0976 – 6464(Print)
ISSN 0976 – 6472(Online)
Volume 5, Issue 2, February (2014), pp. 30-35
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IJECET
©IAEME
GENERATION OF INDICATOR SEQUENCE USING TMS320VC5416
FIXED-POINT DIGITAL SIGNAL PROCESSOR
M. Mohanty1,
Dr. M. Basu2,
Dr. D.N. Pattanayak3
1
Dept.of ETC, Gandhi Engineering College, Madanpur, Bhubaneswar, Odisha, India
Dept.of Power Engg, Jadavpur University, Saltlake campus, Kolkata, West Bengal, India
3
Dept. of EEE, Trident Academy of Tchnology, Infocity Area. Patia, Bhubaneswar, Odisha, India
2
ABSTRACT
The traditional as well as modern signal processing methods are playing an important role in
molecular biology, which is related to the most commonly used terms i.e. DNA (Deoxyribose
Nucleic Acid), gene & Protein. The last few years have seen the blooming of the genomic era, a
period during which a wide range of research effort has been taken on the fractal behavior of DNA
sequences which leads to the research in Genomic signal processing, primarily defined as the
processing of genome sequence that contains the whole hereditary information of a living organism,
encoded in the DNA. This paper concerns with a brief review of some fundamentals related to
molecular biology followed by the implementation of Digital Signal Processor (DSP) for the
processing of DNA sequence. The flexibility of the design & presence of on-chip memory in the
DSP reduces the memory access time as compared to general purpose microprocessor or the
microcontroller.
Keywords: DNA, DSP, CCS.
INTRODUCTION
Recently, signal processing is booming as the most highlighted field approaching towards the
detection, prediction and classification of genetic regulatory networks that are capable of modeling
genetic behavior. It is a method of extracting information from the signal which, in turn, depends
upon the type of signal and the nature of information it carries. Therefore, the signal processing is
concerned with the representation, transformation, and manipulation of signals and the information
they contain [1]. The Genomic Signal Processing (GSP) has been defined as the processing of
genomic signals and its use for gaining biological knowledge and the translation of that knowledge
into system based applications [11]. The aim of GSP is to integrate the theory and methods of signal
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2. International Journal of Electronics and Communication Engineering & Technology (IJECET), ISSN 0976 –
6464(Print), ISSN 0976 – 6472(Online), Volume 5, Issue 2, February (2014), pp. 30-35 © IAEME
processing with the global understanding of functional genomics, with special emphasis on genomic
regulation.
In a very real sense, it must be specified that genomic information is digital in nature, is
represented in the form of sequence. A DNA sequence is a double helical structure, has been
mathematically represented by character string, which is made from an English alphabet of four
elements, namely A, T, C, and G, shown in fig. 1. The letter A, T, C, G represents molecules called
nucleotides or bases as shown in fig 1. ‘A’ is known as Adenine, ‘T’ as Thymine, ‘C’ as Cytosine
and ‘G’ as Guanine. The main role of DNA is the long-term storage of information and for
constructing other components of cells, such as proteins and RNA (Ribose Nucleic Acid) molecules,
as it contains the essential instructions.
Fig.1: Structure of DNA containing the nucleotides
The example of a part of DNA sequence is shown in “(1)”.
…..ATCGGATTCCAGTGAC… (1)
The double helical structure of DNA straightened out for simplicity, demonstrating a simple
schematic diagram for part of a DNA molecule as shown in fig. 2 [18-20]. The base ‘A’ of one
strand is always pairs with ‘T’ of other strand and similarly ‘C’ of one strand always pairs with ‘G’
of other strand. Therefore the number of nucleotides ‘A’ and ‘T’ always same in a DNA sequence
similarly for ‘G’ and ‘C’. This type of pairing is called the Watson and Crick base pairing. Therefore,
the DNA sequence of each organism is represented by the number of base pairs. Since DNA contains
the genetic information of living organisms, so life is governed by quaternary codes [18].
Fig.2: The DNA double helix (linearized schematic)
A DNA sequence can be separated into two types of regions: genes and intergenic spaces.
Again, gene has two types of sub regions called the exons and introns as shown in fig. 3. However,
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3. International Journal of Electronics and Communication Engineering & Technology (IJECET), ISSN 0976 –
6464(Print), ISSN 0976 – 6472(Online), Volume 5, Issue 2, February (2014), pp. 30-35 © IAEME
genes carry the coding information for the generation of proteins. Basically exons region is
responsible for that purpose.
In this paper, an attempt has been made for the processing of a particular DNA sequence with
the Texas Instrument TMS320VC5416 Digital Signal Processor (DSP)[12]. The special reason for
selecting this platform is its advanced modified Harvard architecture having huge computational
power along with the fast processing capability that facilitate the implementation process efficiently
in comparison with the general purpose processor[8-10] and micro controllers[14]. TMS320VC5416
Digital Signal Processor is a 16 bit fixed point Complex Instruction Set Computer (CISC) processor.
Mostly, in the commercial field, the 16-bit processor is used from the cost effective point of view.
The modified Harvard architecture of the DSP provides the pipelining operation which is absent in
the Von Neumann architecture of the general-purpose processors [12-14]. The pipelining property of
the processor reduces the execution time of the instruction as more than one instruction is processed
parallely. Therefore, the digital signal processor is mostly used for the real time application [2,5,12].
Fig.3: DNA sequence showing exons (protein coding region) and introns
Another remarkable advantage of implementing the TMS320VC5416 digital signal processor
is that, the processor facilitates quick implementation of algorithm with the help of Code Composer
Studio (CCS) Integrated Development Environment (IDE) [15-17]. The modification of algorithm
and design parameter need not require any change in the hardware as the digital signal processor is
programmable. So just by reprogramming the source code, the modification can be done.
TMS320VC5416 is a widely used processor for in lab research purpose which is also called Million
Floating Point Processor (MFLOPS), makes it ideal candidate for this work. The choice of
TMS320VC5416 processor has provided flexibility and has considerably saved time for
experimental analysis.
GENERATION OF INDICATOR SEQUENCE
A single DNA strand is represented as a sequence of four nucleotides, namely Adenine (A),
Cytosine (C), Thymine (T), and Guanine (G). For the application in the digital signal processing field
it is necessary to convert the character string of the DNA sequence into a set of digital signals.
Basically, the indicator sequence indicates the location of each nucleotide in the long DNA sequence.
For example, Let the DNA sequence is ATCTAGCTACTAGG…………(1)
So, the corresponding indicator sequence for the base A, represented as xA(n), in the binary form is,
xA(n)=10001000100100……
(2)
n→ length of the DNA sequence or it can be said the number of bases present in the DNA sequence.
In the equation (1), ‘1’ indicates the presence of A and ‘0’ indicates its absence. The indicator
sequences for the other bases are defined similarly.
In this work, the original DNA sequence is broken down into four binary sequences of same length
for four nucleotides, so that, the corresponding binary sequence of each nucleotide will indicate its
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4. International Journal of Electronics and Communication Engineering & Technology (IJECET), ISSN 0976 –
6464(Print), ISSN 0976 – 6472(Online), Volume 5, Issue 2, February (2014), pp. 30-35 © IAEME
position in the original sequence. It is carried out on a particular organism i.e. Bovine gastrine gene
of Bovgas having 1066 base pairs.
FLOW CHART
The flow chart explains the important steps of the program. It gives the brief idea about the
logic for developing the program using TMS320VC5416 processor to generate the indicator
sequence for each nucleotide.
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5. International Journal of Electronics and Communication Engineering & Technology (IJECET), ISSN 0976 –
6464(Print), ISSN 0976 – 6472(Online), Volume 5, Issue 2, February (2014), pp. 30-35 © IAEME
EXPERIMENTAL RESULT
After the successful downloading of the program into the program memory of the processor,
an input window will be displayed on the screen, where we can give the input. Then the input will be
where
processed through the processor, so that, a Stdout tab is opened at the bottom of the window to show
the corresponding output which is sent to stdout by the program. A part of the DNA sequence of
Bovgas is taken for experimental purpose for the ease of checking on the screen, whose
aken
corresponding four indicator sequences are shown in the Fig. 4.
Fig 4: The generation of indicator sequence for Bovgas
In the program, the length is taken as a variable, so that we can take any length of sequence
according to the requirement.
CONCLUSION
This paper eyes on making Genetic Studies easier in the hardware platform for the processing
of DNA sequence. This successful hardware implementation of Generation of indicator sequence has
essful
opened the gates for research works in integrating them into Real-time applications. One aspect of
Real time
this work is to provide a method for identifying and to locate genes or genomic region of interest in
regions
the genome. Another aspect is to provide a method for identifying genetic associations and
converting information into an appropriate data format so that it could be used in practical
applications such as identification of disease
disease-causing genes in complex diseases, in population
population-based
association study, a family-based association study, or a traditional linkage study.
based
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