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
 6
 7
 9
 12 
Axít nuclêic và Nuclêôtít 12 1.1.
Prôtêin và axít amin 15 1.2.
 16 1.3.
 18 1.4.
 19 1.5.
 20 1.6.
 24 1.7.
  26 
 26 2.1.
 28 2.2.
 30 2.3.
 30 2.3.1.
 31 2.3.2.
 34 2.3.3.
 37 2.3.4.
 38 2.4.
CSDL Protei 40 2.5.
 41 2.6.
 42 2.7.

 43 2.8.
 44 2.9.
 46 
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 46 3.1.
 50 3.2.
 53 3.3.
 57 3.4.
 59 3.5.
 64 
 64 4.1.
 65 4.2.
 67 4.3.
 68 4.3.1.
 75 4.3.2.
 77 4.4.
 80 
 80 5.1.
 80 5.1.1.
 81 5.1.2.
 82 5.1.3.
 84 5.1.4.
 86 5.2.
 89 5.3.

 92 5.4.
 92 5.4.1.
 93 5.4.2.
 94 5.4.3.
 94
5.4.4.
 96 5.5.
 96 5.5.1.
 98 5.5.2.
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 99 5.5.3.
 100 5.6.
 100 5.6.1.
 103 5.6.2.
 107 5.7.
 112 
 112 6.1.
Cây phân loài 115 6.2.
 115 6.2.1.
 116 6.2.2.
 117 6.2.3.
 119 6.2.4.
 121 6.3.
 122 6.4.

 127 6.5.
 131 6.6.
 131 6.6.1.
 132 6.6.2.
 133 6.6.3.
 134 6.6.4.
  134 6.7.
 135 6.8.
 136 6.9.
 139 
 139
7.1.
 141 7.2.
-Joining 145 7.3.
 155 7.4.
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 158 
 158 8.1.
 159 8.2.
 159 8.2.1.
 163 8.3.
-Cantor 163 8.3.1.
 164 8.3.2.
 166 8.3.3.

 167 8.3.4.
 168 8.3.5.
 171 8.4.
 173 8.5.
 176 
 176 9.1.
 177 9.2.
ý 183 9.3.
 187 9.4.
BLOSUM 187 9.4.1.
 188 9.4.2.
Mô hình  189 9.4.3.
 190 9.4.4.
 191 9.4.5.
 192 9.5.
 194 
 194
10.1.
 195 10.2.
 195 10.2.1.
 196 10.2.2.
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 198 10.3.
 199 10.4.

 200 10.5.
IQPNNI 200 10.5.1.
PhyML 204 10.5.2.
 207 10.6.
 209 
 209 11.1.
 210 11.2.
-Fasman 212 11.3.
OR 218 11.4.
 222 11.5.
 222 11.5.1.
 224 11.5.2.
 226 11.6.
 227 11.7.


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Danh sách ký hiu và kí t vit tt

, ví d  là tp các nuclêôtít

Chui nuclêôtít/chui axít amin

Ti


S ng các chui

 p hàng

Cây phân loài
ML

MP
 (maximum parsimony)

Ma trn t bii tc thì gia các nuclêôtít hay axít amin

n s xut hin ca các nuclêôtít hay axít amin

Ma trn h s i (exchangeability matrix) gia các nuclêôtít
hay gia các axít amin.




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  
Bioinformatics


Molecular biology

Nucleic acid
Axít nuclêic
DNA
ADN
RNA
ARN
Nucleotide
Nuclêôtít
Protein
Prôtêin
Amino acid
Axít amin
Gene
Gen
Genome

Chromosome
Nh
Accession number

Substitution

Mutation

Transcription
Phiên mã
Translation


Maximum likelihood

Maximum parsimony

Phylogenetic tree
Cây phân loài
Model
Mô hình
Sequence

Pairwise alignment


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Local pairwise alignment

Multiple sequence alignment


Rate matrix

Instantaneous substitution rate matrix


Exchangeability matrix

Frequency vector

Distance matrix



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
 ,
- khoa
. Vin
 



 

và ng internet.



bà

. Giáo trình

                
 

1  

              
nuclêôtít, axít aminnuclêôtít
nuclêôtít. 


 

           ung vào  
 (NCBI), 
Draft version - Confidential


Giáo trình Nmôn tin sinh 


10
nhanh chóng 
.

T
toán trên  

4 trình bày các 

  
                
nhanh chóng  .
bài toán C
. P
 
.
6 

 
các 

              


-

bày nuclêôtít 
nuclêôtít khác nhau 
 nuclêôtít lý
.
axít amin
bày axít amin 
axít amin axít amin 
 ít amin
.
10  


Draft version - Confidential



Giáo trình Nmôn tin sinh 


11


              
prôtêin prôtêin. Bài toán 

 

N   
 C.
 C

 
các 
 

trong giáo trình.
 
tìm  các  




 


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 
 (molecular biology) là  (biology),
 . 
 nuclêôtít ADN), các
axít amin prôtêin)
khác quá trình
 . 
 ADNtính toán 
phân tích  

chúng tôi   
 
 .
Axít nuclêic và Nuclêôtít 1.1.
Axít nuclêic (nucleic acid)         biological
mã hóa 
     .        xít Deoxyribo
Nuclêic (ADN) và ARN (Axít Ribo Nuclêic).
Th  axít nuclêic c
nuclêotít (nucleotide). C ADN   nuclêôtít khác nhau là: Adenine,
Cytosine, Guanine, và Thymine. 
ADN
 Adenine, Cytosine, Guanine, và Uracil. 

 nuclêôtít 1.1.

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
Tên vit tt
Cu trúc
Adenine
A

Cytosine
C

Guanine
G

Thymine
T

Uracil
U

1.1: T   nuclêôtít.
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Hình 1.1ADN.

Các nuclêôtít  ADN 
Hình 1.1 (cADN 
b ). C    
 ADN 
 nuclêôtít 
nuclêôtít 
 Nuclêôtít A nuclêôtít T
 Nuclêôtít nuclêôtít C.
ADN nuclêôtít
nuclêôtít 
 ADN  
A, C, G, và T nuclêôtít)
CAGTTGACGGCGAACCGTGCGAGCAGACGGTCGTT  ADN. 
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ADN và

.
Prôtêin và axít amin 1.2.
in (protein) 
,  
 . Prôtêin axít
amin axít amin 
 chính là: nhóm amin (NH2), nhóm cacboxyl (COOH) và nhóm
R  (xem Hình 1.2).

Hình 1.2

1.2


  
khác nhau
ESPQIRRDMGRLCATWPSKDSEDGAGTALRAATPLTANGATTTGLSVTLAPK
CQTNWDECWSSPCQNGGTCVDGVAYYNCTCPEGFSGSNCEENVDE


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STT
Tên axít amin
Tên vit tt (3 ký t)

Tên vit tt (1 ký t)
1
Alanine
Ala
A
2
Arginine
Arg
R
3
Asparagine
Asn
N
4
Aspartic
Asp
D
5
Cysteine
Cys
C
6
Glutamine
Gln
Q
7
Glutamic
Glu
E
8

Glycine
Gly
G
9
Histidine
His
H
10
Isoleucine
Ile
I
11
Leucine
Leu
L
12
Lysine
Lys
K
13
Methionine
Met
M
14
Phenylalanine
Phe
F
15
Proline
Pro

P
16
Serine
Ser
S
17
Threonine
Thr
T
18
Tryptophan
Trp
W
19
Tyrosine
Tyr
Y
20
Valine
Val
V
1.2.
Gen và mADN và  prôtêin 1.3.
ADN  
, trong khi prôtêin quy
ADN prôtêin 
 prôtêin
prôtêin  ADN   ADN thông qua quá trình
 prôtêin (Hình 1.3)ADN  ADN mang thông tin
prôtêin  gen. 

ADNgen.
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Hình 1.3prôtêin ADN

Quá trình tprôtêin ADN : Phiên mã
(transcription) (translation) Hình 1.3.
  ADN 
prôtêin  ARN. ARN có
nuclêôtít 
thành nuclêôtít 

ARN 
 ARN 
quy tnuclêôtít  (codon) ARN 
1.3.

axít amin
axít amin, axít aminaxít
aminARN  GAG CCA ACU AUU GAU 
i axít amin  
61   
(start codon).  AUG mã hóa axít amin Met (M) là  


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T

C

A

G



Codon
Axít
amin
Codon
Axít
amin
Codon
Axít
amin
Codon
Axít

amin

T
TTT
Phe
TCT
Ser
TAT
Tyr
TGT
Cys
T
TTC
Phe
TCC
Ser
TAC
Tyr
TGC
Cys
C
TTA
Leu
TCA
Ser
TAA
STOP
TGA
STOP
A

TTG
Leu
TCG
Ser
TAG
STOP
TGG
Trp
G
C
CTT
Leu
CCT
Pro
CAT
His
CGT
Arg
T
CTC
Leu
CCC
Pro
CAC
His
CGC
Arg
C
CTA
Leu

CCA
Pro
CAA
Gln
CGA
Arg
A
CTG
Leu
CCG
Pro
CAG
Gln
CGG
Arg
G
A
ATT
Ile
ACT
Thr
AAT
Asn
AGT
Ser
T
ATC
Ile
ACC
Thr

AAC
Asn
AGC
Ser
C
ATA
Ile
ACA
Thr
AAA
Lys
AGA
Arg
A
ATG
Met
ACG
Thr
AAG
Lys
AGG
Arg
G
G
GTT
Val
GCT
Ala
GAT
Asp

GGT
Gly
T
GTC
Val
GCC
Ala
GAC
Asp
GGC
Gly
C
GTA
Val
GCA
Ala
GAA
Glu
GGA
Gly
A
GTG
Val
GCG
Ala
GAG
Glu
GGG
Gly
G

1.3 nuclêôtít (codon) thành axít amin
nuclêôtít/axít amin theo IUPAC 1.4.
nuclêôtít axít
amin               
nuclêôtít hay axít amin 
IUPAC (International Union of Pure ADN 
u nuclêôtít 1.4.

Tên vit tt

R
G hoc A
Y
T hoc C
K
G hoc T
M
A hoc C
S
G hoc C
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W
A hoc T
B

G hoc T hoc C
D
G hoc A hoc T
H
A ho
V
G hoc C hoc A
N
A hoc G hoc C hoc T
1.4nuclêôtít

t 
các axít amin 1.5.

Tên vit tt (1 ký t)

Z
Glutamine hoc Glutamic
X
Mt trong 20 loi axít amin
B
Asparagine hoc Aspartic
U
Mt trong 20 loi axít amin
1.5
 1.5.
             
ADNprôtêin histone 
       ADN     ADN trong 
           nuclêôtít  


nuclêôtít (xem Hình 1.4).

Hình 1.4 l


gen khác nhau. Hai


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Hình 1.4
  ADN 1.6.
 [1] thì các loài sin
 (xem  Hình 1.5). 


  ADN (hay hai
ADN)  
ADN ADN
   ADN 
nuclêôtít 
ADN              
nuclêôtít 

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Hình 1.5:  
ai prôtêin 
ADN 
prôtêin 

Quá trình bN: nuclêôtít
 (hay các axít amin  axít amin)  Ba

 Thay th (mutation): nuclêôtít nuclêôtít khác.
 Xoá (deletion):  nuclêôtít b    ADN;    
ADN 
 Chèn (insertion): Mnuclêôtít  ADN; 
ADN 

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Hình 1.6ADN

Hình 1.6 minh ha quá trình bii ca hai chui   =
  mt chui ADN t tiên chung   . Ta thy
nuclêôtít C  v trí th 2 ca chui  b xóa khi chui ; và nuclêôtít T  v trí
th 8 ca chui  b thay th bng nuclêôtít G  chui .
Khi so sánh trc tip hai chui  và , chúng 
       t phép bi i gia hai chui  và ; hoc mt
nuclêôtít  xóa khi chui ; hoc nuclêôtít c chèn thêm vi
chui . Do không có thông tin v chui ADN t tiên chung , chúng ta
n ra  v trí
này, vì v i ta gi phép bi i này là phép bi i chèn/xóa
(indel).
 Ti v trí th 8 có mt phép thay th nuclêôtít gia hai chui  và .
Nuclêôtít T  chui  nuclêôtít G 

Các phép ADN  gen
Các  
 gen khác nhau.  
, 
 gen  vào . 
.

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prôtêin: nuclêotít ADN
trong quá trình tin hóa s d n các bi i trên các chui axít amin mà
chúng mã hóa. Các bii gia hai chui prôtêin  xut hin trong
quá trình tng hp prôtêin t các chui ADN. Ví d hai chui ADN ng 
     = CCTGAGCCAACTGAT" s mã
hóa hai prôtêin ng   = PEPTV (xem 1.6).


1
2
3
4
5
6
7
Chui ADN 
CCT
GAG
CCA
ACT
ATT
GAT
GAA
Chui ADN 
CCG
GAG
CCA
ACT
ATT
GTT

  








Chui prôtêin 
P
E
P
T
I
D
E
Chui prôtêin 
P
E
P
T
I
V










1.6: Các bii gia hai chui ADN và hai chui prôtêin ng
ca chúng.

So sánh hai chui ADN  prôtêin ng  ca chúng, ta
nhn thy:
 Có mt phép thay th nuclêôtít  v trí th 3 ca codon th nht gia hai
chui ADN  và 

hóa axít amin P).
 Có mt phép thay th nuclêôtít  v trí th 2 ca codon th 6 gia hai chui
ADN  và . Phép thay th này dn s bii ca hai axít amin do
ng; axít amin D trên prôtêin  
i prôtêin , hoc li.
 Có mt phép chèn/xóa codon  v trí th 7 gia hai chui ADN  và .
Phép chèn/xóa này dn mt phép chèn/xóa axít amin  v trí th 7 gia
hai chui prôtêin ng  và 
7 trên chui prôtêin ; hoc m xóa khi v trí th 7
trên chui prôtêin .

ADN 

các prôtêin 
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  1.7.
1. ADN . 
  ADN.
2. khác nhau i vi mt
nuclêôtít trên mt chui ADN.
3. Cho hai chui ADN
 A
 GGTGGGCCCTG
Hãy tìm các phép bii khi so sánh hai chui này.
4. Cho hai chui ADN
 
 

5. Mnuclêôtít, 

6.  
nuclêôtít mã hóa cho 
7. ADN sang prôtêin
ADN  thành prôtêin hay không?
8. Tìm và trình bày các thông tin sau:
 
  
 
 
9. Tìm và trình bày các thông tin sau:
 
 
 nhim sc th trong b gen ca con chó

 S ng nhim sc th trong b gen ca cây lúa
10. Cho n gen
Draft version - Confidential


Giáo trình Nmôn tin sinh 


25
CGCCCCCGTTCCCTGGGTGTT
. Hãy tìm chui axít amin  ng vi n  này.
11. Cho chui prôtêin  = , h kê tt c các n gen có th mã hóa
prôtêin  trên.
12. Cho chui prôtêin  = , hãy lit kê tt c các n gen có th mã hóa
prôtêin  trên.
13. 
vào ADN_protein nucleotít 
kì (c  
).

file ADN_protein
  
cho các nuclêôtít, thì  ra màn hình.


ADN_protein.in
ADN_protein.out
CAGTTGACGGCGAACCGT
QLTANR