Origin of Replication - I
Signals and Systems in Biology
Kushal Shah @ EE, IIT Delhi
DNA Replication
Bacterial DNA
Ori : Some facts
I
Replication may proceed uni-directionally or bi-directionally
I
Usually AT-rich region
I
Bacteria : circular DNA and single origin of replication
I
Archaea : Circular DNA and multiple origins
I
Eukaryotes : Linear DNA and multiple origins
I
I
Firing time of each Ori may be different
Modeling of this ’firing’ phenomenon is a challenging task
Ori : Some facts
I
Replication may proceed uni-directionally or bi-directionally
I
Usually AT-rich region
I
Bacteria : circular DNA and single origin of replication
I
Archaea : Circular DNA and multiple origins
I
Eukaryotes : Linear DNA and multiple origins
I
I
Firing time of each Ori may be different
Modeling of this ’firing’ phenomenon is a challenging task
Ori : Some facts
I
Replication may proceed uni-directionally or bi-directionally
I
Usually AT-rich region
I
Bacteria : circular DNA and single origin of replication
I
Archaea : Circular DNA and multiple origins
I
Eukaryotes : Linear DNA and multiple origins
I
I
Firing time of each Ori may be different
Modeling of this ’firing’ phenomenon is a challenging task
Ori : Some facts
I
Replication may proceed uni-directionally or bi-directionally
I
Usually AT-rich region
I
Bacteria : circular DNA and single origin of replication
I
Archaea : Circular DNA and multiple origins
I
Eukaryotes : Linear DNA and multiple origins
I
I
Firing time of each Ori may be different
Modeling of this ’firing’ phenomenon is a challenging task
Ori : Some facts
I
Replication may proceed uni-directionally or bi-directionally
I
Usually AT-rich region
I
Bacteria : circular DNA and single origin of replication
I
Archaea : Circular DNA and multiple origins
I
Eukaryotes : Linear DNA and multiple origins
I
I
Firing time of each Ori may be different
Modeling of this ’firing’ phenomenon is a challenging task
Ori : Some facts
I
Replication may proceed uni-directionally or bi-directionally
I
Usually AT-rich region
I
Bacteria : circular DNA and single origin of replication
I
Archaea : Circular DNA and multiple origins
I
Eukaryotes : Linear DNA and multiple origins
I
I
Firing time of each Ori may be different
Modeling of this ’firing’ phenomenon is a challenging task
Ori : Some facts
I
Replication may proceed uni-directionally or bi-directionally
I
Usually AT-rich region
I
Bacteria : circular DNA and single origin of replication
I
Archaea : Circular DNA and multiple origins
I
Eukaryotes : Linear DNA and multiple origins
I
I
Firing time of each Ori may be different
Modeling of this ’firing’ phenomenon is a challenging task
Ori : Some facts
I
Replication may proceed uni-directionally or bi-directionally
I
Usually AT-rich region
I
Bacteria : circular DNA and single origin of replication
I
Archaea : Circular DNA and multiple origins
I
Eukaryotes : Linear DNA and multiple origins
I
I
Firing time of each Ori may be different
Modeling of this ’firing’ phenomenon is a challenging task
Ori : Cell Cycle
I
I
I
I
G1 phase : Initiation of major replication regulatory processes
S phase : Actual DNA replication
G2 phase : Correction of replication errors or other damages
M phase : Segregation of parent cell into daughters
Prokaryotic cell : ~ 20 mins
Eukaryotic cell : ~ 18 to 24 hrs!
Ori : Cell Cycle
I
I
I
I
G1 phase : Initiation of major replication regulatory processes
S phase : Actual DNA replication
G2 phase : Correction of replication errors or other damages
M phase : Segregation of parent cell into daughters
Prokaryotic cell : ~ 20 mins
Eukaryotic cell : ~ 18 to 24 hrs!
Ori : Cell Cycle
I
I
I
I
G1 phase : Initiation of major replication regulatory processes
S phase : Actual DNA replication
G2 phase : Correction of replication errors or other damages
M phase : Segregation of parent cell into daughters
Prokaryotic cell : ~ 20 mins
Eukaryotic cell : ~ 18 to 24 hrs!
Ori : Cell Cycle
I
I
I
I
G1 phase : Initiation of major replication regulatory processes
S phase : Actual DNA replication
G2 phase : Correction of replication errors or other damages
M phase : Segregation of parent cell into daughters
Prokaryotic cell : ~ 20 mins
Eukaryotic cell : ~ 18 to 24 hrs!
Ori : Cell Cycle
I
I
I
I
G1 phase : Initiation of major replication regulatory processes
S phase : Actual DNA replication
G2 phase : Correction of replication errors or other damages
M phase : Segregation of parent cell into daughters
Prokaryotic cell : ~ 20 mins
Eukaryotic cell : ~ 18 to 24 hrs!
Ori : Cell Cycle
I
I
I
I
G1 phase : Initiation of major replication regulatory processes
S phase : Actual DNA replication
G2 phase : Correction of replication errors or other damages
M phase : Segregation of parent cell into daughters
Prokaryotic cell : ~ 20 mins
Eukaryotic cell : ~ 18 to 24 hrs!
Ori : Cell Cycle
I
I
I
I
G1 phase : Initiation of major replication regulatory processes
S phase : Actual DNA replication
G2 phase : Correction of replication errors or other damages
M phase : Segregation of parent cell into daughters
Prokaryotic cell : ~ 20 mins
Eukaryotic cell : ~ 18 to 24 hrs!
Ori : Prokaryotes
I
Circular DNA and single origin of replication
I
9-mer and 13-mer repeats
I
I
DnaA box (4 nos.): 5’ - TTATCCACA - 3’
DnaB box (3 nos.): 5’ - GATCTNTTNTTTT - 3
I
DnaA protein binds to 9-mers & simulates the 13-mers to unwind
I
DnaC loads the DnaB to each of the two unwound strands
I
SSB prevents single strands from forming secondary structures
I
DNA gyrase relieves the stress!
Ori : Prokaryotes
I
Circular DNA and single origin of replication
I
9-mer and 13-mer repeats
I
I
DnaA box (4 nos.): 5’ - TTATCCACA - 3’
DnaB box (3 nos.): 5’ - GATCTNTTNTTTT - 3
I
DnaA protein binds to 9-mers & simulates the 13-mers to unwind
I
DnaC loads the DnaB to each of the two unwound strands
I
SSB prevents single strands from forming secondary structures
I
DNA gyrase relieves the stress!
Ori : Prokaryotes
I
Circular DNA and single origin of replication
I
9-mer and 13-mer repeats
I
I
DnaA box (4 nos.): 5’ - TTATCCACA - 3’
DnaB box (3 nos.): 5’ - GATCTNTTNTTTT - 3
I
DnaA protein binds to 9-mers & simulates the 13-mers to unwind
I
DnaC loads the DnaB to each of the two unwound strands
I
SSB prevents single strands from forming secondary structures
I
DNA gyrase relieves the stress!
Ori : Prokaryotes
I
Circular DNA and single origin of replication
I
9-mer and 13-mer repeats
I
I
DnaA box (4 nos.): 5’ - TTATCCACA - 3’
DnaB box (3 nos.): 5’ - GATCTNTTNTTTT - 3
I
DnaA protein binds to 9-mers & simulates the 13-mers to unwind
I
DnaC loads the DnaB to each of the two unwound strands
I
SSB prevents single strands from forming secondary structures
I
DNA gyrase relieves the stress!
Ori : Prokaryotes
I
Circular DNA and single origin of replication
I
9-mer and 13-mer repeats
I
I
DnaA box (4 nos.): 5’ - TTATCCACA - 3’
DnaB box (3 nos.): 5’ - GATCTNTTNTTTT - 3
I
DnaA protein binds to 9-mers & simulates the 13-mers to unwind
I
DnaC loads the DnaB to each of the two unwound strands
I
SSB prevents single strands from forming secondary structures
I
DNA gyrase relieves the stress!
Ori : Prokaryotes
I
Circular DNA and single origin of replication
I
9-mer and 13-mer repeats
I
I
DnaA box (4 nos.): 5’ - TTATCCACA - 3’
DnaB box (3 nos.): 5’ - GATCTNTTNTTTT - 3
I
DnaA protein binds to 9-mers & simulates the 13-mers to unwind
I
DnaC loads the DnaB to each of the two unwound strands
I
SSB prevents single strands from forming secondary structures
I
DNA gyrase relieves the stress!
Ori : Prokaryotes
I
Circular DNA and single origin of replication
I
9-mer and 13-mer repeats
I
I
DnaA box (4 nos.): 5’ - TTATCCACA - 3’
DnaB box (3 nos.): 5’ - GATCTNTTNTTTT - 3
I
DnaA protein binds to 9-mers & simulates the 13-mers to unwind
I
DnaC loads the DnaB to each of the two unwound strands
I
SSB prevents single strands from forming secondary structures
I
DNA gyrase relieves the stress!
Ori : Prokaryotes
I
Circular DNA and single origin of replication
I
9-mer and 13-mer repeats
I
I
DnaA box (4 nos.): 5’ - TTATCCACA - 3’
DnaB box (3 nos.): 5’ - GATCTNTTNTTTT - 3
I
DnaA protein binds to 9-mers & simulates the 13-mers to unwind
I
DnaC loads the DnaB to each of the two unwound strands
I
SSB prevents single strands from forming secondary structures
I
DNA gyrase relieves the stress!
Ori : Prokaryotes
I
Circular DNA and single origin of replication
I
9-mer and 13-mer repeats
I
I
DnaA box (4 nos.): 5’ - TTATCCACA - 3’
DnaB box (3 nos.): 5’ - GATCTNTTNTTTT - 3
I
DnaA protein binds to 9-mers & simulates the 13-mers to unwind
I
DnaC loads the DnaB to each of the two unwound strands
I
SSB prevents single strands from forming secondary structures
I
DNA gyrase relieves the stress!
Prokaryotic DNA Replication
Occurs inside the cytoplasm
Only one origin of replication
Ori length about 100-200 nt
DnaA and DnaB boxes
Initiation by DnaA and DnaB
Replication is very rapid
Eukaryotic DNA replication
Occurs inside the nucleus
Have many origins of replication
Each Ori of about 150 nt
No conserved consensus sequence
(S. cerevisiae : WTTTAYRTTTW)
W=A/T, Y=C/T, T=A/G
Initiation by ORC protein
Replication is very slow
Prokaryotic DNA Replication
Occurs inside the cytoplasm
Only one origin of replication
Ori length about 100-200 nt
DnaA and DnaB boxes
Initiation by DnaA and DnaB
Replication is very rapid
Eukaryotic DNA replication
Occurs inside the nucleus
Have many origins of replication
Each Ori of about 150 nt
No conserved consensus sequence
(S. cerevisiae : WTTTAYRTTTW)
W=A/T, Y=C/T, T=A/G
Initiation by ORC protein
Replication is very slow
Prokaryotic DNA Replication
Occurs inside the cytoplasm
Only one origin of replication
Ori length about 100-200 nt
DnaA and DnaB boxes
Initiation by DnaA and DnaB
Replication is very rapid
Eukaryotic DNA replication
Occurs inside the nucleus
Have many origins of replication
Each Ori of about 150 nt
No conserved consensus sequence
(S. cerevisiae : WTTTAYRTTTW)
W=A/T, Y=C/T, T=A/G
Initiation by ORC protein
Replication is very slow
Prokaryotic DNA Replication
Occurs inside the cytoplasm
Only one origin of replication
Ori length about 100-200 nt
DnaA and DnaB boxes
Initiation by DnaA and DnaB
Replication is very rapid
Eukaryotic DNA replication
Occurs inside the nucleus
Have many origins of replication
Each Ori of about 150 nt
No conserved consensus sequence
(S. cerevisiae : WTTTAYRTTTW)
W=A/T, Y=C/T, T=A/G
Initiation by ORC protein
Replication is very slow
Prokaryotic DNA Replication
Occurs inside the cytoplasm
Only one origin of replication
Ori length about 100-200 nt
DnaA and DnaB boxes
Initiation by DnaA and DnaB
Replication is very rapid
Eukaryotic DNA replication
Occurs inside the nucleus
Have many origins of replication
Each Ori of about 150 nt
No conserved consensus sequence
(S. cerevisiae : WTTTAYRTTTW)
W=A/T, Y=C/T, T=A/G
Initiation by ORC protein
Replication is very slow
Prokaryotic DNA Replication
Occurs inside the cytoplasm
Only one origin of replication
Ori length about 100-200 nt
DnaA and DnaB boxes
Initiation by DnaA and DnaB
Replication is very rapid
Eukaryotic DNA replication
Occurs inside the nucleus
Have many origins of replication
Each Ori of about 150 nt
No conserved consensus sequence
(S. cerevisiae : WTTTAYRTTTW)
W=A/T, Y=C/T, T=A/G
Initiation by ORC protein
Replication is very slow
Prokaryotic DNA Replication
Occurs inside the cytoplasm
Only one origin of replication
Ori length about 100-200 nt
DnaA and DnaB boxes
Initiation by DnaA and DnaB
Replication is very rapid
Eukaryotic DNA replication
Occurs inside the nucleus
Have many origins of replication
Each Ori of about 150 nt
No conserved consensus sequence
(S. cerevisiae : WTTTAYRTTTW)
W=A/T, Y=C/T, T=A/G
Initiation by ORC protein
Replication is very slow
Prokaryotic DNA Replication
Occurs inside the cytoplasm
Only one origin of replication
Ori length about 100-200 nt
DnaA and DnaB boxes
Initiation by DnaA and DnaB
Replication is very rapid
Eukaryotic DNA replication
Occurs inside the nucleus
Have many origins of replication
Each Ori of about 150 nt
No conserved consensus sequence
(S. cerevisiae : WTTTAYRTTTW)
W=A/T, Y=C/T, T=A/G
Initiation by ORC protein
Replication is very slow
How long does the replication process take?
I
Speed
I
I
I
Prokaryotes : 1000 nt per second
E. coli ∼ 4000kb ⇒ 4000 seconds
Eukaryotes : 50 nt per second
If only one origin was present, time ~ 35 days!!
Presence of multiple Ori reduces overall time.
Error Rate
I
I
I
I
Error during replication is about 1 per 100000 nt
Humans: 6 billion nt ⇒ 60000 errors!!
Error Correcting Mechanism : Proof-reading and Mismatch repair
Reported final error rates : 10−9 to 10−2
Not all errors are bad!!
How long does the replication process take?
I
Speed
I
I
I
Prokaryotes : 1000 nt per second
E. coli ∼ 4000kb ⇒ 4000 seconds
Eukaryotes : 50 nt per second
If only one origin was present, time ~ 35 days!!
Presence of multiple Ori reduces overall time.
Error Rate
I
I
I
I
Error during replication is about 1 per 100000 nt
Humans: 6 billion nt ⇒ 60000 errors!!
Error Correcting Mechanism : Proof-reading and Mismatch repair
Reported final error rates : 10−9 to 10−2
Not all errors are bad!!
How long does the replication process take?
I
Speed
I
I
I
Prokaryotes : 1000 nt per second
E. coli ∼ 4000kb ⇒ 4000 seconds
Eukaryotes : 50 nt per second
If only one origin was present, time ~ 35 days!!
Presence of multiple Ori reduces overall time.
Error Rate
I
I
I
I
Error during replication is about 1 per 100000 nt
Humans: 6 billion nt ⇒ 60000 errors!!
Error Correcting Mechanism : Proof-reading and Mismatch repair
Reported final error rates : 10−9 to 10−2
Not all errors are bad!!
How long does the replication process take?
I
Speed
I
I
I
Prokaryotes : 1000 nt per second
E. coli ∼ 4000kb ⇒ 4000 seconds
Eukaryotes : 50 nt per second
If only one origin was present, time ~ 35 days!!
Presence of multiple Ori reduces overall time.
Error Rate
I
I
I
I
Error during replication is about 1 per 100000 nt
Humans: 6 billion nt ⇒ 60000 errors!!
Error Correcting Mechanism : Proof-reading and Mismatch repair
Reported final error rates : 10−9 to 10−2
Not all errors are bad!!
How long does the replication process take?
I
Speed
I
I
I
Prokaryotes : 1000 nt per second
E. coli ∼ 4000kb ⇒ 4000 seconds
Eukaryotes : 50 nt per second
If only one origin was present, time ~ 35 days!!
Presence of multiple Ori reduces overall time.
Error Rate
I
I
I
I
Error during replication is about 1 per 100000 nt
Humans: 6 billion nt ⇒ 60000 errors!!
Error Correcting Mechanism : Proof-reading and Mismatch repair
Reported final error rates : 10−9 to 10−2
Not all errors are bad!!
How long does the replication process take?
I
Speed
I
I
I
Prokaryotes : 1000 nt per second
E. coli ∼ 4000kb ⇒ 4000 seconds
Eukaryotes : 50 nt per second
If only one origin was present, time ~ 35 days!!
Presence of multiple Ori reduces overall time.
Error Rate
I
I
I
I
Error during replication is about 1 per 100000 nt
Humans: 6 billion nt ⇒ 60000 errors!!
Error Correcting Mechanism : Proof-reading and Mismatch repair
Reported final error rates : 10−9 to 10−2
Not all errors are bad!!
How long does the replication process take?
I
Speed
I
I
I
Prokaryotes : 1000 nt per second
E. coli ∼ 4000kb ⇒ 4000 seconds
Eukaryotes : 50 nt per second
If only one origin was present, time ~ 35 days!!
Presence of multiple Ori reduces overall time.
Error Rate
I
I
I
I
Error during replication is about 1 per 100000 nt
Humans: 6 billion nt ⇒ 60000 errors!!
Error Correcting Mechanism : Proof-reading and Mismatch repair
Reported final error rates : 10−9 to 10−2
Not all errors are bad!!
How long does the replication process take?
I
Speed
I
I
I
Prokaryotes : 1000 nt per second
E. coli ∼ 4000kb ⇒ 4000 seconds
Eukaryotes : 50 nt per second
If only one origin was present, time ~ 35 days!!
Presence of multiple Ori reduces overall time.
Error Rate
I
I
I
I
Error during replication is about 1 per 100000 nt
Humans: 6 billion nt ⇒ 60000 errors!!
Error Correcting Mechanism : Proof-reading and Mismatch repair
Reported final error rates : 10−9 to 10−2
Not all errors are bad!!
How long does the replication process take?
I
Speed
I
I
I
Prokaryotes : 1000 nt per second
E. coli ∼ 4000kb ⇒ 4000 seconds
Eukaryotes : 50 nt per second
If only one origin was present, time ~ 35 days!!
Presence of multiple Ori reduces overall time.
Error Rate
I
I
I
I
Error during replication is about 1 per 100000 nt
Humans: 6 billion nt ⇒ 60000 errors!!
Error Correcting Mechanism : Proof-reading and Mismatch repair
Reported final error rates : 10−9 to 10−2
Not all errors are bad!!
How long does the replication process take?
I
Speed
I
I
I
Prokaryotes : 1000 nt per second
E. coli ∼ 4000kb ⇒ 4000 seconds
Eukaryotes : 50 nt per second
If only one origin was present, time ~ 35 days!!
Presence of multiple Ori reduces overall time.
Error Rate
I
I
I
I
Error during replication is about 1 per 100000 nt
Humans: 6 billion nt ⇒ 60000 errors!!
Error Correcting Mechanism : Proof-reading and Mismatch repair
Reported final error rates : 10−9 to 10−2
Not all errors are bad!!
How long does the replication process take?
I
Speed
I
I
I
Prokaryotes : 1000 nt per second
E. coli ∼ 4000kb ⇒ 4000 seconds
Eukaryotes : 50 nt per second
If only one origin was present, time ~ 35 days!!
Presence of multiple Ori reduces overall time.
Error Rate
I
I
I
I
Error during replication is about 1 per 100000 nt
Humans: 6 billion nt ⇒ 60000 errors!!
Error Correcting Mechanism : Proof-reading and Mismatch repair
Reported final error rates : 10−9 to 10−2
Not all errors are bad!!
How long does the replication process take?
I
Speed
I
I
I
Prokaryotes : 1000 nt per second
E. coli ∼ 4000kb ⇒ 4000 seconds
Eukaryotes : 50 nt per second
If only one origin was present, time ~ 35 days!!
Presence of multiple Ori reduces overall time.
Error Rate
I
I
I
I
Error during replication is about 1 per 100000 nt
Humans: 6 billion nt ⇒ 60000 errors!!
Error Correcting Mechanism : Proof-reading and Mismatch repair
Reported final error rates : 10−9 to 10−2
Not all errors are bad!!
Ori finding method : Skews
I
Chargaff’s Parity Rule : A ≈ T and G ≈ C for whole genome
Used by Watson and Crick in their discovery of DNA structure
I
Over smaller windows, G 6= C and A 6= T
I
I
Different mutational pressures on the leading and lagging strand
due to difference in replication machinery
Difference in selective pressures
due to inhomogeneous distribution of genes
Ori finding method : Skews
I
Chargaff’s Parity Rule : A ≈ T and G ≈ C for whole genome
Used by Watson and Crick in their discovery of DNA structure
I
Over smaller windows, G 6= C and A 6= T
I
I
Different mutational pressures on the leading and lagging strand
due to difference in replication machinery
Difference in selective pressures
due to inhomogeneous distribution of genes
Ori finding method : Skews
I
Chargaff’s Parity Rule : A ≈ T and G ≈ C for whole genome
Used by Watson and Crick in their discovery of DNA structure
I
Over smaller windows, G 6= C and A 6= T
I
I
Different mutational pressures on the leading and lagging strand
due to difference in replication machinery
Difference in selective pressures
due to inhomogeneous distribution of genes
Ori finding method : Skews
I
Chargaff’s Parity Rule : A ≈ T and G ≈ C for whole genome
Used by Watson and Crick in their discovery of DNA structure
I
Over smaller windows, G 6= C and A 6= T
I
I
Different mutational pressures on the leading and lagging strand
due to difference in replication machinery
Difference in selective pressures
due to inhomogeneous distribution of genes
Ori finding method : Skews
I
Chargaff’s Parity Rule : A ≈ T and G ≈ C for whole genome
Used by Watson and Crick in their discovery of DNA structure
I
Over smaller windows, G 6= C and A 6= T
I
I
Different mutational pressures on the leading and lagging strand
due to difference in replication machinery
Difference in selective pressures
due to inhomogeneous distribution of genes
Ori finding method : Skews
I
Chargaff’s Parity Rule : A ≈ T and G ≈ C for whole genome
Used by Watson and Crick in their discovery of DNA structure
I
Over smaller windows, G 6= C and A 6= T
I
I
Different mutational pressures on the leading and lagging strand
due to difference in replication machinery
Difference in selective pressures
due to inhomogeneous distribution of genes
Ori finding method : Skews
I
Chargaff’s Parity Rule : A ≈ T and G ≈ C for whole genome
Used by Watson and Crick in their discovery of DNA structure
I
Over smaller windows, G 6= C and A 6= T
I
I
Different mutational pressures on the leading and lagging strand
due to difference in replication machinery
Difference in selective pressures
due to inhomogeneous distribution of genes
Ori finding method : Skews
I
Chargaff’s Parity Rule : A ≈ T and G ≈ C for whole genome
Used by Watson and Crick in their discovery of DNA structure
I
Over smaller windows, G 6= C and A 6= T
I
I
Different mutational pressures on the leading and lagging strand
due to difference in replication machinery
Difference in selective pressures
due to inhomogeneous distribution of genes
GC skew and Sliding window method
ATATGTAGCAGTGAGTACGAGATCGAGAGTCGAGA
ATATGTAGCAGTGAGTACGAGATCGAGAGTCGAGA
ATATGTAGCAGTGAGTACGAGATCGAGAGTCGAGA
ATATGTAGCAGTGAGTACGAGATCGAGAGTCGAGA
C −G
C +G
J. R. Lobry, Science 1996
J. Mrazek and S. Karlin, PNAS 1998
A−T
A+T
GC Skew
0.06
E. coli
0.04
(C-G)/(G+C)
0.02
0
-0.02
-0.04
-0.06
-0.08
0
Arrow : ter
50
100
150
200 250 300
Window Number
Entropy?
350
400
450
500
CGC : Cumulative GC skew
A. Grigoriev, Nucleic Acids Research 1998
Z-curve method
xn
yn
zn
= (An + Gn ) – (Cn + Tn )
= (An + Cn ) – (Gn + Tn )
= (An + Tn ) – (Cn + Gn )
R. Zhang and C. T. Zhang, BBRC 2002
C (k ) =
(C-G)/(G+C)
Correlation :
0.2
0.15
0.1
0.05
0
-0.05
-0.1
-0.15
Correlation (CG)
0.55
0.5
0.45
0.4
0.35
0.3
0.25
0.2
CG = ∑ |C (k )|
k =1
B. subtilis
(a)
0
N −1
1 N −k
aj aj +k
N − k j∑
=1
50
100
150
200
250
300
Window Number
350
400
450
400
450
B. subtilis
(b)
0
50
100
150
200
250
300
Window Number
350
K. Shah and A. Krishnamachari, BioSystems 2012
C (k ) =
(C-G)/(G+C)
Correlation :
0.4
0.3
0.2
0.1
0
-0.1
-0.2
1 N −k
aj aj +k
N − k j∑
=1
Correlation (CG)
50
0.88
0.86
0.84
0.82
0.8
0.78
0.76
0.74
0.72
0.7
100
150
200
Window Number
250
300
P. falciparum apicoplast
(b)
0
k =1
P. falciparum apicoplast
(a)
0
N −1
CG = ∑ |C (k )|
50
100
150
200
Window Number
K. Shah and A. Krishnamachari, BioSystems 2012
250
300