Research Article |
Open Access |
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Matrix Frequency Analysis of Oryza Sativa
(japonica cultivar-group) Complete Genomes |
K. Manikandakumar 1,*, S. Muthu Kumaran 2, R. Srikumar 3 |
1Department of Physics, Bharathidasan University College (W), Orathanadu – 614 625,
Tanjavore District, Tamil Nadu, India |
2Department of Physics, Nehru Memorial College, Puthanampatti – 621 007,
Tiruchirappalli District,
Tamil Nadu, India |
3Department of Microbiology, Bharathidasan University College (W), Orathanadu – 614 625,
Tanjavore District, Tamil Nadu, India |
| *Corresponding author: |
Dr. K. Manikandakumar, Department of Physics,
Bharathidasan University College (W), Orathanadu – 614 625, Tanjavore District,
Tamil Nadu, India,
Phone : 9787383327
E-mail : bioinfokm@gmail.com |
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| Received January 28, 2009; Accepted April 20, 2009; Published April 22, 2009 |
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Citation: Manikandakumar K, Kumaran MS, Srikumar R (2009) Matrix Frequency Analysis of Oryza Sativa (japonica
cultivar-group) Complete Genomes. J Comput Sci Syst Biol 2: 159-166. doi:10.4172/jcsb.1000027 |
| |
Copyright: © 2009 Manikandakumar K, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author
and source are credited. |
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The genome sequence information is essential to understand the function of extensive arrangements of genes. It is
significant to combine all sequence information in a precise database to provide an efficient manner of sequence
similarity search. The complete genome analysis, which is one of the essential steps to know their characteristics, is
very important. Complete genome analysis is depends on matrix frequency of sequence residue calculation and CGR
analysis. In this study, we select rice as the specimen for complete genome analysis. Rice is one of the most essential
cereal crops providing food for more than half of the world’s population. Oryza sativa (japonica cultivar-group)
species is an important cereal and model monocot. We have generated a matrix frequency for genetic code analysis,
which helps in the study of complete genome residues. Here we report the duplets and triplets codon for genetic code
analysis of O. sativa chromosomes. We illustrate a new method of Chaos Game Representation, which produces the
objects possessing self-similar structure. As per our findings, the average matrix frequency of stop codons is similar
to the matrix frequency of start codon. This average is seems to be similar in the complete genome sequences of every
Oryza sativa (japonica cultivar-group) chromosomes. |
Keywords |
| Oryza sativa (japonica cultivar-group); Chaos game representation; chromosome; matrix frequency; fractal
structure |
Introduction |
DNA is a double anti-parallel helix built by concatenating
nucleotide blocks. Several physicochemical properties
of DNA depends on the interactions between consecutive
bases, thus, the classification of patterns from nearest neighbor
bases could help in the description of nucleotide sequences
( Mohanty A. K and A.V.S.S. Narayana Rao, 2000).
However, ( Almeida J. S et al, 2001) have followed the scale
independence of CGR of genetic sequence method to investigate
local and global homology. The two patterns identified from the analysis of whole genomes and the number
of different dinucleotides are unequal frequencies of manifestation
of some asymmetric pairs and preferences of certain
nucleotides with specific nearest neighbors over equivalent
dinucleotides ( Nussinov R, 1980, 1981). |
Small plant chromosomes, such as those in rice, often
show irregular condensation at mitotic prometaphase. Thus,
the condensation pattern appearing at prometaphase was only a morphological landmark to divide the rice chromosomes
into sub-regions. Characteristics of each rice chromosome
with uneven condensation have quantitatively been
analyzed by using image analysis methods. (Fukui K, 1985,
Iijima K and Fukui K, 1991) developed a method for identifying
rice chromosomes based on a flow chart that consists
of 11 discriminates, which classify specific chromosome
groups. All rice chromosomes have identified and
numbered by comparing the categories given by discriminates,
one after another. The chromosomal spread is worth
analyzing if, chromosomes 4, 11, and 12 are distinguishable
by visual inspection and if chromosomes 1, 2, and 3
are completely recognized. If these six chromosomes are
identified using discriminates 1 to 6 in order, then there is a
great possibility of identifying all 12 chromosomes within
the particular spread. The relevance of accessing the frequency
of non-integer genomic sequences may not be apparent
at first given that (Almeida J. S et al, 2001) physically
make all sequences of integer number of nucleotides. |
The genome sequence information is indispensable in
understanding the function of the wide array of genes that
constitute the rice plant. Therefore, it is important to consolidate
all sequence information in a specified database to
provide an efficient method of sequence similarity search
that eliminates artifactual matches be analysed by (Yoshiaki
Nagamura et al, 2003). We have generated a matrix frequency
for genetic code analysis with all available rice genome
for Oryza sativa japonica-cultivar group. (Li-Zhi Gao
et al, 2005) analysed that DNA shuffling is a direct evolution
process which generates genetic diversity through the
recombination of parental sequences in order to evaluate
which pair of sequences could potentially produce the best
result. Oryza sativa (japonica cultivar-group), a subspecies
of rice, is an important cereal and model monocot
(35884299 bp). The rice genome sequence provides a foundation
for the improvement of cereals, our most important
crops (Stephen A et al, 2002). Experiments of direct evolution
have successfully used to improve specific biological
functions. (Jorge Luis Fuentes et al, 2005) analyses Genetic
diversity of rice varieties (Oryza sativa L.) based on
morphological, pedigree and DNA polymorphism data,
Plant Genetic Resources and phenotypic, genealogical,
RAPD and AFLP diversity groups. |
Mathematical characterization of DNA sequences could
help in the understanding of structural relationships among
different whole genomes along the chromosomes. The degenerated
translation of trinucleotide codons encode for 20
amino acids, and remaining three nonsense codons signal
for the end of transcription. Base concentrations, stretches
and patches are the main factors explaining the variability
observed among sequences (Deschavanne P. J et al 1999).
The genomic signature as expressed in terms of short nucleotide usage extends and generalizes the genomic signature
and it takes advantages of whole genome data reveals genome
wide trends (Karlin S and Burge C, 1995). The measure
of similarity using CGR can be the basis of a new set
of algorithms to align sequences with considerable advantages
over the conventional scoring methods (Almeida J. S
et al, 2001). The CGR is a formalism that bridges between
sequence of discrete units and numeric coordinates in a
continuous space. Consequently, basic statistic measures
and techniques have applied to sequences and a wide range
of new tools have devised for statistical analysis. Here we
report the genetic code analysis of complete genome of all
chromosomes of O. sativa. We have generated a matrix
frequency of the rice genome. We describe a new method
of Chaos Game Representation applied to O. Sativa
(japonica cultivar-group) species sequences, which produces
fractal objects possessing self-similar structure. |
Material and Methods |
| The Oryza sativa (japonica cultivar-group) Eukaryote
complete genomes have downloaded from the GOLD (http://www.genomesonline.org/) database. The species have been
totally 12 chromosomes. The details of the chromosomes
are giving below. |
[http://www.genomesonline.org/gold.cgi?want=
Published+Co plete+Genomes] |
|
A simple model, which permits the simulation of these
features of nucleotide residues, is discrete time Markov
Chain (Goldman N, 1993). In this model, a 4 X 4 matrix, P
defines the probabilities with which subsequent bases follow
the current base in a nucleotide residue. If the base
labels A,T,G, and C are equated with the numbers 1,2,3 and
4; then Pij is the jth element of the ith row of P which defines
the probability that base j follows base i. The row sums of
P must equal 1. Using this matrix, a simulated nucleotide
residue may be obtained by selecting a first base randomly
according to the frequencies of the bases in the nucleotide
residue under study. If the base is i, then the probabilities
will be Pi1, Pi2, Pi3 and Pi4. These probabilities are used to
select the next base, and so on until the simulated sequence
is the same length as the original nucleotide residues. |
This first-order Markov Chain model is in which successive
bases in a residue depend only on the preceding base.
The probabilities in the matrix P may be estimated by direct
calculation from the residues dinucleotide frequencies.
If the dinucleotide XY is observed nxy times in the sequence,
then probability Pxy is estimated by nxy / (nXA + nXT + nXG + nXC). This permits a protein sequence to be simulated with
both individual base frequencies and digroup frequencies
matching those of the original sequence. Dinucleotide frequencies
(nXY) and Markov Chain probabilities (PXY) for
the Oryza sativa (japonica cultivar-group) genomes are
given in Table - 2. |
The first-order Markov Chain model successfully recreates
other genomes. The lack of banding suggests approximate
equality of the frequencies of the bases A, C, G, and T,
confirmed by direct calculation from the residues. The firstorder
Markov Chain model will not give the observed patterns,
but a more complex second-order Markov Chain, in
which each base depends on the previous two, does. Second-
order Markov Chains have been used to describe both
structure and with-in-structure of nucleotide residues. PXYZ,
the probability that base Z follows the trigroup XYZ, is
estimated directly from the nucleotide residues trigroup frequencies
nXYZ using the formula PXYZ = nXYZ / (nXYA + nXYT +
nXYG + nXYC). Trinucleotide frequencies (nXYZ) and Markov
Chain probabilities (PXYZ) for the Oryza sativa (japonica
cultivar-group) genomes are given in Table - 3. |
We apply the CGR method to Oryza sativa (japonica cultivar-
group) species by considering the four different nucleotide
residues into four groups namely Adenine, Thymine,
Guanine and Cytosine. Using this distinctive way of CGR
technique, the Oryza sativa (japonica cultivar-group) species
produces the intrinsic fractal structure. The percentage
values of nucleotide residues of the four groups available in the species under consideration has also computed and
used for analysis. We find that some of the species of Oryza
sativa (japonica cultivar-group) nucleotide sequences produce
the similar kind of self-similar fractal structure. The
CGR shows the characteristics of the Oryza sativa (japonica
cultivar-group) genome. |
To begin with, let us generate the typical fractal object
namely the ‘Square’ possessing the self-similar structure
using the Chaos Game Representation (CGR). Let us start
with three vertices located at (0,0), (1,0), (0,1) and (1,1)
labeled as A, T, C and G respectively. Now random sequences
of 1, 2, 3 and 4 are obtained using a random number
generator available in typical C compiler. In generating
CGR, the nth point of the attractor is simply the midpoint
between the (n-1)th point and the vertex corresponding
to the nth value. Similarly, the successive application of
this procedure for 100,000 points produces the ‘Square’ as
shown in Fig. 1, which is a typical fractal object possessing
self-similar structure. |
We calculate the nucleotide contents of the above species
into grouping of four types name as A, T, G and C. Used in
computer algorithm the nucleotide contents are differentiating
to each group. Then we calculate the A+G and T+C
ratios of the above species. Finally, the average ratio of the
each chromosome is calculating by the method A+G/T+C.
All the results are given by percentage values. The Table-1
is given by all the chromosome details of the Oryza sativa
(japonica cultivar-group) species. The CGR plots are drawn
using Gnu plot method. |
Pictorial Representation |
Chaos Game Representation (CGR) for gene (or DNA)
sequences was introduced by (Jeffrey H. J, 1990, 1992) and
the essential structures of genome sequences of a few model
organisms were obtained using CGR plots. Each chromosome
has been taken in above 200,000 base pairs. Therefore,
we did not represent the whole genomes. We have
taken only first 100,000 base pairs nucleotide sequences
for the above representation. |
Results and Discussions |
The structure of DNA is specific to each species and undergoes
only slight variations along the whole genome
(Deschavanne P. J et al, 1999). Diversity among species is
considerable and is primarily a consequence of base concentration,
stretches of bases with unusual frequencies. The
frequencies of occurrence are to point out the basis of the
genome (Deschavanne P. J et al, 1999). In our analysis is
giving the matrix frequency calculation of every chromosome complete genome sequences. We analysed every chromosome
and given in the Table - 1 is shown by the individual
nucleotide contents percentage. The table - 2 has
shown by the first order Markov chain matrix frequency of
all chromosomes and it is representing in dinucleotide
codons. The Table - 3 is show by the second order Markov
chain matrix frequency of all chromosomes and it is representing
in trinuclotide codons. The Table – 4 is shown, the
classification of triplets to occurring in which regions. The
Table - 5 is shown by the relations of the start and stop
codons of all chromosomes. |
We analyze the complete genome of Oryza sativa
(japonica cultivar-group) species chromosomes nucleotide
contents and the calculation is giving in Table - 1. From
the table-1, the chromosome 4 has been largest residues
(17028043 base pairs). The lowest residues have been chromosome
11 (298736 base pairs). Chromosome no. 1 is having
the lowest Adenine residues (26.99%) and chromosome
10 is having the highest adenine residues (28.84%). The
range of Thymine residues is 27.81% got the chromosome
no. 9 and 28.73% of thymine residues are having chromosome
no.10. The range of Guanine ratio is 21.36% (chromosome
5) and 22.70 (chromosome 1). The range of Cytosine
ratio is 21.19% (chromosome 10) and 22.16 (chromosome
1). The range of A+G content ratio is 49.55%
(chromosome 3) and 50.18% (chromosome 2). The range
of T+C content ratio is 49.82% (chromosome 2) and 50.45%
(chromosome 3). The chromosome 8 has been representing
in same nucleotide content ratio in Guanine and Cytosine
residues (21.57%). |
We generate and analyse the first order Markov chain
matrix frequency for 16 (4 x 4) nucleotide doublet codons
for Oryza sativa (japonica cultivar-group) species complete
genome chromosomes and the matrix frequency for each
doublet codon is given in Table-2. The Table-2 has shown,
the AA codon minimum frequency range is 0.299 for chromosome-
1 and the maximum frequency range is 0.321 for
chromosome-10. The CA codon minimum frequency range
is 0.289 for chromosome-1 and the maximum frequency
range is 0.317 for chromosome-5. The GA codon minimum
frequency range is 0.271 for chromosome-3 and the
maximum frequency range is 0.285 for chromosome-5. The
TA codon minimum frequency range is 0.223 for chromosome-
1 and the maximum frequency range is 0.245 for chromosome-
7. The AC codon minimum frequency range is
0.179 for chromosome-10 & 11 and the maximum frequency
range is 0.189 for chromosome-3. The CC codon minimum
frequency range is 0.232 for chromosome-2 and the
maximum frequency range is 0.249 for chromosome-4. The
GC codon minimum frequency range is 0.229 for chromosome-
10 and the maximum frequency range is 0.248 for
chromosome-3. The TC codon minimum frequency range
is 0.223 for chromosome-1 and the maximum frequency
range is 0.207 for chromosome-11. The AG codon minimum
frequency range is 0.204 for chromosome-10 and the
maximum frequency range is 0.224 for chromosome-1. The
CG codon minimum frequency range is 0.160 for chromosome-
5 and the maximum frequency range is 0.192 for chromosome-
4 & 6. The GG codon minimum frequency range
is 0.233 for chromosome-12 and the maximum frequency
range is 0.250 for chromosome-9. The TG codon minimum
frequency range is 0.221 for chromosome-10 and the
maximum frequency range is 0.248 for chromosome-1. The
AT codon minimum frequency range is 0.283 for chromosome-
6 & 9 and the maximum frequency range is 0.296 for
chromosome-10. The CT codon minimum frequency range
is 0.266 for chromosome-4 and the maximum frequency
range is 0.289 for chromosome-11. The GT codon minimum
frequency range is 0.235 for chromosome-9 and the
maximum frequency range is 0.245 for chromosome-10.
The TT codon minimum frequency range is 0.306 for chromosome-
1 and the maximum frequency range is 0.320 for
chromosome-8. |
We have generate and analyse the second order Markov
chain matrix frequency for 64 (4 x 4 x 4) nucleotide triplet
codons for Oryza sativa (japonica cultivar-group) species
complete genome chromosomes and the matrix frequency
for each tripet codon is given in Table-3. From Table-3,
most of the highest nucleotide triplet codon is representing
in AAA and TTT. The most of the lowest nucleotide triplets
are AGC and TGC. All the above chromosomes, we
identify the low sparseness regions are mostly played in
species of triplets as AC-A,T; GCA, TC-A,T; AG-A,C, CGA,
T; GGC, TGA and TGC respectively. The highest sparseness
regions are mostly played in species of triplets as AAA,
C,G; CA-A,C; GAA, ATT, CTT, GTT and TT-A,T respectively. |
Table-4 has shown the frequency triplet codons have separated
by four regions. The regions are classifying the frequency
range of 0.125-0.199, 0.200-0.249, 0.250-0.299, and
above 0.300 matrix frequency of triplet codons. This table
is easy to analyse and to study, how many tripets are coming
under particular range of frequency. |
We have analysed the relations between the start codon
and stop codon frequencies and it has given in Table-5. The
genetic code is show in three types of stop codons. But the
start codon is only one. Therefore, we tried to show one
stop codon for every sequence. Our analysis has not succeeded.
Nevertheless, the average of two-stop codon value is nearly equal to the start codon. This Table-4 is describes,
separated and shown in start and stop codon for each chromosomes
in Oryza sativa (japonica cultivar-group). This
table shows every start codon frequency is equal to the average
of two-stop codon frequency. So this analysis is used
to finding and expressed the start codon is equal to stop
codon for every Oryza sativa (japonica cultivar-group) chromosome
complete genome sequences. |
The figure 1, is shown the CGR plot for the first 100,000
base pairs of 12 chromosomes of Oryza sativa (japonica
cultivar-group) species, we identify the genomes are cross
overlapping in A, G and T, C. Four triangles are connecting
in the mid point of 0.5, 0.5, 0.5, and 0.5 respectively.
The A-T region is keeping in more numbers of residues. |
Analysis of Individual Chromosome |
Chromosome 1 |
The chromosome 1 is, total of 301936 base pairs. From
the Table-1, the highest percentage value is Thymine residue
(28.15%). The lowest percentage value is Cytosine
residue (22.16%). The Adenine and Guanine residues are
26.99% and 22.70%. The highest combination of nucleotide
residues of T+C percentage is 50.31%. The ratio of
A+G & T+C is 1.0. The triplet of chromosome 1, the highest
tri-nucleotide is TTT (0.348%). The lowest tri-nucleotide
is AGC (0.163%). From the Table-3, the matrix frequency
of chromosome 1, high frequency of tri-nucleotide
sequence has been representing in AAA, AAC, TTA, and
TTT (above 0.300%). Tri-nucleotide sequence of 0.250%
to 0.299% has been represented in AAG, AAT, CA-A,C,G;
GA-A,C,G; TA-A,C,G; CC-G,T; GC-C,G; TC-C,G; AGT,
CGG, GG-A,T; AT-A,C,T; CT-A,C,T; GT-A,C,T; TT-C,G.
Tri-nucleotide sequence of 0.200% to 0.249% has been represented
in CAT, GAT, TAT, AC-C,G,T; CC-A,C; GC-G,T;
TC-G,T; AG-A,G; CG-A,C,T; GGG, TG-A,G,T; ATG,CTG
and GGG. Tri-nucleotide sequence of 0.150% to 0.199%
is representing in ACA, GCA, TCA, AGC, GGC, and TGC. |
Chromosome 2 |
The chromosome 2 is total of 662387 base pairs. The
highest percentage value is Adenine residue (28.39%). The
lowest percentage value is Guanine residue (21.79%). The
Thymine and Cytosine residues are 27.98% and 21.84%.
The highest combination of nucleotide residues of A+G
percentage is 50.18%. The ratio of A+G & T+C content is
1.0. The triplet codon of chromosome 2, the highest triplet
is AAA (0.351%). The lowest triplet codon is TGC
(0.157%). |
The matrix frequency of chromosome 2, the frequency of
tri-nucleotide sequence has been represented in AA-A,C,G;
CA-A,C; GAC, TAC, TT-A,T (above 0.300%). Tri-nucleotide
sequence of 0.250% to 0.299% has been represented
in AAT, CAG, GA-A,G; TA-A,G; CC-G,T; GCG, CGG, GGA,
T; AT-A,C,T; CT-A,C,T; GT-A,C,T; TT-C,G. Tri-nucleotide
sequence of 0.200% to 0.249% has been represented
in CAT, GAT, TAT, AC-C,G,T; CCC, GC-C,T; TC-C,G,T;
AG-A,G,T; CG-A,T; GGG, TG-G,T; ATG,CTG and GTG.
Tri-nucleotide sequence of 0.150% to 0.199% has been representing
in ACA, CCA, GCA, TCA, AGC, CGC, GGC,
TGA, and TGC. |
Chromosome 3 |
| The chromosome 3 is total of 831805 base pairs. The
highest percentage value is Thymine residue (28.34%). The
lowest percentage value is Guanine residue (22.05%). The
Adenine and Cytosine residues are 27.50% and 22.11%.
The highest combination of nucleotide residues of T+C
percentage is 50.45%. The ratio of A+G & T+C content is
1.0. The triplet codon of chromosome 3, the highest triplet
is TTT (0.355%). The lowest triplet codon is TGC (0.162%). |
The matrix frequency of chromosome 3, the frequency of
tri-nucleotide sequence has been represented in AA-A,C;
GTT, TT-A,C,T (above 0.300%). Tri-nucleotide sequence
of 0.250% to 0.299% has been represented in AA-G,T, CAA,
C, GA-A,C,G; TA-A,C,G; CC-G,T; GC-C,G, CGG, GGA,
T; AT-A,C,T; CT-A,C,T; GT-A,C; TTG. Tri-nucleotide
sequence of 0.200% to 0.249% has been represented in CAG,
T; GAT, TAT, AC-C,G,T; CC-A,C; GCT, TC-C,G,T; AGA,
G,T; CG-A,C,T; GGG, TG-G,T; ATG,CTG and GTG. Trinucleotide
sequence of 0.150% to 0.199% has been representing
in ACA, GCA, TCA, AGC, GGC, TGA and TGC. |
Chromosome 4 |
The chromosome 4 is total of 17028043 base pairs. The
highest percentage value is Thymine residue (27.95%). The
lowest percentage value is Cytosine residue (22.08%). The
Adenine and Guanine residues are 27.88% and 22.10%.
The highest combination of nucleotide residues of T+C
percentage is 50.03%. The ratio of A+G & T+C is 1.0. The
triplet codon of chromosome 4, the highest triplet is AAA
(0.347%). The lowest triplet codon is AGC (0.169%). The
matrix frequency of chromosome 4, the frequency of trinucleotide
sequence has been represented in AA-A,C; CAA,
CTT, TT-A,T (above 0.300%). Tri-nucleotide sequence of
0.250% to 0.299% has been represented in AA-G,T, CAC,
G; GA-A,C,G; TA-A,C,G; CCT, GC-G,T; TCC, CGG,
GG-A,T; TGG, AT-A,C,T; CT-A,C; GT-A,C,T; TT-C,G. Tri-nucleotide sequence of 0.200% to 0.249% has been represented
in CAT, GAT, TAT, AC-C,G,T; CC-A,C,G; GCT, TCG,
T; AG-A,G,T; CG-C,T; GG-C,G, TG-A,T; ATG, CTG and
GTG. Tri-nucleotide sequence of 0.150% to 0.199% has
been representing in ACA, GCA, TCA, AGC, CGA, and
TGC. |
Chromosome 5 |
The chromosome 5 is total of 476423 base pairs. The
highest percentage value is Adenine residue (28.61%). The
lowest percentage value is Guanine residue (21.36%). The
Thymine and Cytosine residues are 28.47% and 21.55%.
The highest combination of nucleotide residues of T+C
percentage is 50.02%. The ratio of A+G & T+C content is
1.0. The triplet codon of chromosome 5, the highest triplets
is AAA and TTT (0.354%). The lowest triplet codon is
AGC (0.143%). The matrix frequency of chromosome 5,
the frequency of tri-nucleotide sequence has been represented
in AA-C,G; CA-A,C; GA-A,C(same ratio); TAC &
TTC are the same ratio. CTT, GTT, TT-A; AAA and TTT
are the same ratio of nucleotides (above 0.300%). Tri-nucleotide
sequence of 0.250% to 0.299% has been represented
in AAT, CAG; GAG; TA-A,G; CC-G,T, GCG=TCC; CGG,
GG-A,T; AT-A,C,T; CT-A,C; GT-A,C; TTG. Tri-nucleotide
sequence of 0.200% to 0.249% has been represented in CAT,
GAT, TAT, AC-C,G,T; CCC, GC-C,T, TC-G,T; AG-A,G,T;
CG-A,T; GGG, TG-G,T; ATG, CTG and GTG. Tri-nucleotide
sequence of 0.150% to 0.199% has been representing
in ACA, CCA, GCA, TCA, AGC, CGC, GGC and TGC. |
Chromosome 6 |
The chromosome 6 is total of 1949261 base pairs. The
highest percentage value is Adenine residue (28.03%). The
lowest percentage value is Cytosine residue (21.88%). The
Thymine and Guanine residues are 27.96% and 22.12%.
The highest combination of nucleotide residues of A+G
percentage is 50.15%. The ratio of A+G & T+C content is
1.0. The triplet codon of chromosome 6, the range of triplets
is TTT (0.359%) and TGC (0.172%). The matrix frequency
of chromosome 6, the frequency of tri-nucleotide
sequence has been represented in AA-A,C,G; CAA, GAA,
GTT, TT-A,T of nucleotides (above 0.300%). Tri-nucleotide
sequence of 0.250% to 0.299% has been represented in AAT,
CA-C,G; GA-C,G; TA-A,C,G; CC-G,T, GC-C,G; CGG, GGA,
T; AT-A,C,T; CT-A,C,T; GT-A,C; TT-C,G. Tri-nucleotide
sequence of 0.200% to 0.249% has been represented in CAT,
GAT, TAT, AC-C,G,T; CC-A,C, GCT, TC-C,G,T; AG-G,T;
CG-A,C,T; GG-C,G, TG-A,G,T; ATG, CTG and GTG. Trinucleotide
sequence of 0.125% to 0.199% has been represented
in ACA, GCA, TCA, AG-A,C and TGC. |
Chromosome 7 |
| The chromosome 7 is total of 993326 base pairs. The
highest percentage value is Adenine residue (28.67%). The
lowest percentage value is Guanine residue (21.47%). The
Thymine and Cytosine residues are 28.24% and 21.63%.
The highest combination of nucleotide residues of A+G
percentage is 50.14%. The ratio of A+G & T+C content is
1.0. The triplet codon of chromosome 7, the frequency of
triplets is AAA (0.361%) and AGC (0.161%). The matrix
frequency of chromosome 7, the frequency of tri-nucleotide
sequence has been represented in AA-A,C,G; CA-A,C; TTA,
T of nucleotides (above 0.300%). Tri-nucleotide sequence
of 0.250% to 0.299% has been represented in AAT, CAG,
GA-A,C,G; TA-A,C,G; CC-G,T, GC-C,G; CGG, GG-A,T;
AT-A,C,T; CT-A,C,T; GT-A,C,T; TT-C,G. Tri-nucleotide
sequence of 0.200% to 0.249% has been represented in CAT,
GAT, TAT, AC-C,G; CC-A,C, GCT, TC-C,G; AG-G,T; CGC,
T; GGG, TG-G,T; ATG, CTG and GTG. Tri-nucleotide
sequence of 0.125% to 0.199% has been represented in ACA,
T; GCA, TC-A,T; AG-A,C, CGA, GGC, TGA and TGC. |
Chromosome 8 |
The chromosome 8 is total of 8367279 base pairs. The
highest percentage value is Adenine residue (28.49%). The
lowest percentage values are represented in Guanine and
Cytosine residues (21.57%). The Thymine residue is
28.37%. The highest combination of nucleotide residues
of A+G percentage is 50.06%. The ratio of A+G & T+C
content is 1.0. The triplet codon of chromosome 8, the range
of triplets is TTT (0.360%) and AGC (0.164%). The matrix
frequency of chromosome 8, the frequency of tri-nucleotide
sequence has been represented in AA-A,C,G; CA-A,C;
GAA, ATT, CTT, GTT, TT-A,T of nucleotides (above
0.300%). Tri-nucleotide sequence of 0.250% to 0.299% has
been represented in AAT, CAG, GA-C,G; TA-A,C,G; CCG,
T, GC-C,G; CGG, GGT, AT-A,C; CT-A,C; GT-A,C; TTC,
G. Tri-nucleotide sequence of 0.200% to 0.249% has been
represented in CAT, GAT, TAT, AC-C,G,T; CC-A,C, GCT,
TC-C,G,T; AG-G,T; CG-C,T; GG-A,G, TG-G,T; ATG, CTG
and GTG. Tri-nucleotide sequence of 0.125% to 0.199%
has been represented in ACA, GCA, TCA, AG-A,C; CGA,
GGC, TGA and TGC. |
Chromosome 9 |
The chromosome 9 is total of 2439243 base pairs. The
highest percentage value is Adenine residue (28.06%). The
lowest percentage value is Guanine residue (22.06%). The
Thymine and Cytosine residues are 27.81% and 22.07%.
The highest combination of nucleotide residues of A+G percentage is 50.12%. The ratio of A+T & G+C is 1.0. The
highest triplets are AAA and TTT (0.346%). The lowest
triplet codon is AGC (0.162%). The matrix frequency of
chromosome 9, the frequency of tri-nucleotide sequence
has been represented in AA-A,C; CA-A,C; CTT, GTT, TTA,
T (above 0.300%). Tri-nucleotide sequence of 0.250%
to 0.299% has been represented in AA-G,T, CAG, GAA,
C,G; TA-A,C,G; CCT, GC-C,G; TCC, CGG, GG-A,T;
AT-A,C,T; CT-A,C; GT-A,C; TT-C,G. Tri-nucleotide sequence
of 0.200% to 0.249% has been represented in CAT,
GAT, TAT, AC-C,G,T; CC-A,C,G; GCT, TC-G,T; AG-A,G,T;
CG-C,T; GGG, TG-A,G,T; ATG, CTG and GTG. Tri-nucleotide
sequence of 0.150% to 0.199% has represented in
ACA, GCA, TCA, AGC, CGA, GGC and TGC. |
Chromosome 10 |
The chromosome 10 is total of 306812 base pairs. The
highest percentage value is Adenine residue (28.84%). The
lowest percentage value is Cytosine residue (21.19%). The
Thymine and Guanine residues are 28.73% and 21.24%.
The highest combination of nucleotide residues of A+G
percentage is 50.08%. The ratio of A+G & T+C content is
1.0. The highest triplet is AAA (0.360%). The lowest triplet
codon is ACA (0.165%). The matrix frequency of chromosome
10, the frequency of tri-nucleotide sequence has
been represented in AA-A,C,G; CA-A,C; GAA, ATT, CTT,
TT-A,T (above 0.300%). Tri-nucleotide sequence of 0.250%
to 0.299% has been represented in AAT, CAG, GA-C,G;
TA-A,C,G; CCT, GCC, CGG, GG-A,T; AT-A,C; CT-A,C;
GT-A,C,T; TT-C,G. Tri-nucleotide sequence of 0.200% to
0.249% has been represented in CAT, GAT, TAT, AC-C,G;
CC-A,C,G; GC-G,T, TC-C,G; AG-G,T; CGC, GGG, TGG,
T; ATG, CTG, GTG. Tri-nucleotide sequence of 0.150%
to 0.199% has been represented in AC-A,T; GCA, TC-A,T;
AG-A,C, CG-A,T; GGC, TGA and TGC. |
Chromosome 11 |
| The chromosome 11 is total of 298736 base pairs. The
highest percentage value of Thymine residue is 28.66%.
The lowest percentage value of Cytosine residue is 21.21%.
The Adenine and Guanine residues are 28.50% and 21.63%.
The highest combination of nucleotide residues of A+G percentage
is 50.13%. The ratio of A+G & T+C content is 1.0.
The highest triplet codon frequency (TTT) is 0.363%. The
lowest triplet codon frequency AGC is 0.146%. The matrix
frequency of chromosome 11, the frequency of tri-nucleotide
sequence has been represented in AA-A,C,G; CA-A,C;
GA-C,G, TAC, GTT, TT-A,C,T (above 0.300%). Tri-nucleotide
sequence of 0.250% to 0.299% has been represented
in AAT, CAG, GAA, TA-A,G; CC-G,T, CGG, GG-A,T; ATA,C,T; CT-A,C,T; GT-A,C; TTG. Tri-nucleotide sequence
of 0.200% to 0.249% has been represented in CAT, GAT,
TAT, AC-C,G; CC-A,C; GC-C,G; TC-C,G; AG-A,G,T; CGA,
T; GGG, TG-A,G,T; ATG, CTG, GTG. Tri-nucleotide
sequence of 0.150% to 0.199% has been represented in ACA,
T; GC-A,T; TC-A,T; AGC, CGC, GGC and TGC. |
Chromosome 12 |
The chromosome 12 is total of 2229048 base pairs. The
highest percentage value of Adenine residue is 28.54%. The
lowest percentage value of Guanine residue is 21.60%. The
Thymine and Cytosine residues are 28.21% and 21.65%.
The highest combination of nucleotide residues of A+G
percentage is 50.14%. The ratio of A+G & T+C content is
1.0. The highest triplet codon frequency of TTT is 0.353%.
The lowest triplet codon frequency of AGC is 0.154%. The
matrix frequency of chromosome 12, the frequency of trinucleotide
sequence has been represented in AA-A,C,G;
CA-A,C; GA-A,C; TAC, TT-A,T (above 0.300%). Trinucleotide
sequence of 0.250% to 0.299% has been represented
in AAT, CAG, GAG; TA-A,G; CC-G,T, GCG, CGG,
GG-A,T; AT-A,C,T; CT-A,C,T; GT-A,C,T; TT-C,G. Trinucleotide
sequence of 0.200% to 0.249% has been represented
in CAT, GAT, TAT, AC-C,G,T; CC-A,C; GC-C,T;
TC-C,G,T; AG-A,G,T; CG-A,T; GGG, TG-A,G,T; ATG,
CTG, GTG. Tri-nucleotide sequence of 0.150% to 0.199%
has represented in ACA, GCA, TCA, AGC, CGC, GGC
and TGC. |
Conclusion |
| The new techniques just described identifying the rice
chromosome and specifying the region using the first order
Markov chain, second order Markov chain and CGR methods
of the DNA sequence analysis. The probabilities defining
these models can calculated directly and easily from
the raw DNA sequences, implying that the CGR gives no
further insight into the structure of the DNA sequence than
is given by the dinucleotide and trinucleotide frequencies.
In this paper, we have shown that simple Markov Chain
models based solely on dinucleotide and trinucleotide frequencies
can account for the complex patterns exhibited in
CGR of Oryza sativa (japonica cultivar-group) chromosome
sequences. The Oryza sativa (japonica cultivar-group) species
chromosome sequences are more similar to each other.
However, our analysis is visible of sequence pattern is similar
in each other. Some high matrix frequency value (0.300)
of tri-nucleotide codon is having by small number of trinucleotides,
but the matrix values are different in each other.
The low-resolution codon frequencies are having by small
number of tri-nucleotides (0.125-0.199), but the matrix value is different. We observed the above results the low-resolution
tri-nucleotides are very low. The chromosome 1 is
having four high frequency (above 0.300%) tri-nucleotides.
The chromosome 8 has been representing in same nucleotide
content ratio in Guanine and Cytosine residues
(21.57%). The frequency matrix values 0.200% to 0.299%
are highly responsible for the Oryza sativa (japonica cultivar-
group) species. It is representing more number of trinucleotide
codons. Finally, we observed the frequency of
start codon is equal to average of two stop codon frequencies.
The in silico analysis of the matrix frequency study is
used in invitro/ invivo studies for reassembling the particular
repaired codon region which is modified by the gene
tinkering (codon replacing) methods. The future analysis
can integrate these procedures into one logical, individual
gene. |
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