Chng 2

NGHIN CU VA PHN TICH

TRINH T NUCLEOTIDE, TRINH T AMINO ACID
(4 tit)
Muc tiu: (1) Nm c nhng c s ct li ca chng trnh x l d liu; (2) Nhn
bit c bi ton t ra trong x l d liu sinh hc; (3) Phn tch, so snh c cc
trnh t bng s dng chng trnh ClustalW trong phn mm BioEdit v DNAstar; (4)
Phn tch c s tng ng ca cc trnh t bng chng trnh BLAST. (5) S dng
thnh tho phn mm so snh trnh t nucleotide v amino acid v phn tch quan h
di truyn da trn trnh t nucleotide v trnh t amino acid.
N i dung
1. C s xy dng chng trnh x l d liu nucleotide v amino acid;
1.1. c im ca trnh t nucleotide: cu truc nucleotide, ma di truyn, qu trnh phin
ma v dich ma, trnh t amino acid
1.2. D li u s cp v th cp v nucleotide: (i) Trnh t nucleotide phn l p; (ii) ng
k trn GenBank, (iii) Trnh t nucleotide trn GenBank; (iv) Trnh t amino acid trn
GenBank.
2. Chng trnh phn tch trnh t nucleotide v amino acid
2.1. Muc tiu cua phn tch trnh t nucleotide v amino acid
- Xc inh s tng ng v sai khc gia cc trnh t;
- Khng inh gen a phn l p ;
- nh gi s a dng trong trnh t nucleotide v amino acid;
- Thit l p s hnh cy v mi quan h gia cc i tng nghin cu;
2.2. Tm kim m t trnh t
Trong nghin cu sinh hc phn t, ngi nghin cu phi thng xuyn lm
vic vi DNA v protein. y l cc trnh t sinh hc c lu tr ph bin trong cc c
s d liu sinh hc NCBI, EMBL, DDBJ. C s d liu ny rt ln v c cp nht
thng xuyn. tm nhng trnh t sinh hc ny, chung ta s dng cng c tm kim
Entrez nucleotide (tm trnh t DNA) hoc Entrez protein (tm trnh t protein).
2.2.1. Cch tm trnh t DNA
T trang NCBI nhn chn Nucleotide a n trang Entrez nucleotide sau nhp
yu cu (thng l tn gen) v nhn nut Go hoc Enter. Kt qu s xut hin mt danh
sch trnh t DNA tng t nh sau:
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Nhn vo mt trnh t c th xem chi tit trnh t nucleotide.

2.2.2. Cch tm trnh t protein

T trang NCBI nhn chn Proten a n trang Entrez protein sau nhp yu cu
(thng l tn protein) v nhn nut Go hoc Enter. Kt qu s xut hin mt danh sch
trnh t protein tng t nh sau:

Nhn vo mt trnh t c th xem chi tit trnh t amino acid.

2.3. Phn tch trnh t bng phn mm

2.3.1. Phn mm BioEdit
Chn biu tng BioEdit v kch up
(1) Nhp d liu

Cc d liu c a vo BioEdit bng cch chuyn t my gii trnh t gen, truy cp

t ngn hng gen hoc nhp d liu th cng.
Cch nhp:
Nhn up chut vo biu tng BioEdit
Chn New Alignment
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Chn menu File Import

La chn trnh t cn a vo so snh v nghin cu

(2) So snh trnh t

Sau khi a d liu vo phn mm, so snh trnh t gen cng nh trnh t amino acid
ta thc hin nh sau:
-

Chn menu Accessory Application

Chn ClustalW Multiple Alignment

Chn Run ClustalW

(3) H s tng ng

bit c h s tng ng ca cc trnh t va so snh th ta thc hin cc bc

nh sau:
-

Thc hin cc bc mc a, b

Chn Alignment

Chn Sequence Identity matrix, ghi tn file v nhn Save

(4) i trnh t nucleotide sang trnh t amino acid

- Thc hin cc bc nh mc a
- Chn menu Sequence
- Chn Translate in selected frame (fermanent)

(5) i trnh t DNA sang RNA

- Thc hin cc bc nh mc a a trnh t DNA vo

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- Chn menu Sequence

- Chn DNARNA

(6) Thit lp bn enzyme ct gii hn

- Thc hin cc bc nh mc a a trnh t nucleotide vo phn mm
- Chn menu Sequence
- Chn Nucleic acid
- Chn Restriction map

(7) Copy d liu so snh

Sau khi so snh trnh t nucleotide hoc trnh t amino acid, nu mun copy d liu
a so snh cn thc hin cc bc sau :
-

Chn File Graphic view

Thay i mt s inh dng theo mong mun nh c ch, phng ch, rng,

Chn Edit Copy page as a bitmap

M Word v dn (Paste)

2.3.2. Phn mm DNAstar

DNAstar l phn mm phn tch, so snh trnh t nucleotide, trnh t amino acid v
phn tch s a dng trong trnh t t nucleotide, trnh t amino acid.
(1) Nh p d li u vo Editseq bng cch ti t GenBank hay nh p th cng.

(2) Chn chng trnh phn tch t biu tng DNAstar

(3) Chn Enter sequences nh p d li u trnh t

(4) Chn Elign, Clustal W method chy chng trnh

(5) Vo View, chn Alignment Report, Sequence Distance, Phylogenetic Tree c
kt qu v so snh cc trnh t, h s tng ng v phn ly, s hnh cy.

2.4. Chng trnh phn tch trnh t nucleotide v amino acid bng BLAST trong
NCBI
2.4.1. i cng v BLAST
BLAST trong NCBI l chng trnh phn tch so snh trnh t nucleotide v
trnh t amino amin xc inh tng ng v khng inh trnh t gen phn l p
(nh n bit gen).
2.4.2. S dung chng trnh BLAST
(i) Blast so snh tng ng v trnh t nucleotide
(1) Vo web http://blast.ncbi.nlm.nih.gov/Blast.cgi, chn BLAST (Choose a BLAST
program to run), nucleotide blast. Ti file cha trnh t nucleotide ho c a trnh t
dng FASTA.

(2) Chy chng trnh Blast: chn BLAST v thu c kt qu:

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(ii) Blast so snh tng ng v trnh t amino acid c tin hnh tng t nh Blast
so snh tng ng v trnh t nucleotide.
4. Phn tch tnh a dng di truyn da trn trnh t nucleotide, amino acid v
on DNA
4.1. Phn tch tnh a dng di truyn da trn trnh t nucleotide, amino acid
4.1.1. Tm trnh t gen ho c protein trong NCBI;
4.1.2. La chn phn mm phn tch (BioEdit ho c DNAstar).
4.1.3. Thit l p bng ma tr n v s hnh cy

4.2. Phn tch tnh a dng di truyn da trn on DNA bng phn mm NTSYS
- Da trn s xut hin hay khng xut hin ca cc phn on ADN khi in di sn
phm RAPD v c nh gi theo quy c: 1-xut hin, 0-khng xut hin.
- Mt bng gm cc gi tri 0 v 1 c thit lp cho php tnh ra h s tng ng di
truyn ca cc cp i tng
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- Thit lp s hnh cy v xc inh quan h h hng ca cc i tng nghin cu

Cc bc thc hin
1. Nhp d liu vo NTEDIT:
a. Chn biu tng NTEDIT
b. Chn s lng hng v ct, t tn cho ct
c. Nhp s liu
d. Chn File v save file (v d tn: DT1)
2. X l d liu
Chn biu tng NTSYS
a. Chn Similarity
- Chn SimQual
- Vo input file (kch up)
- Chn file a t tn DT1
- Vo Output file (kch up), chn DT1 v i thnh DT2
- Save, chn Compute v Close
b. Chn Clusteving
- Chn SAHN
- Chn input, kch up, chn DT2
- Chn Output kch up, chn DT2 v i thnh DT3
- Save, chn Compute
c. Chn Graphics
- Chn Tree plot
- Vo input file chn DT3
- Nhn Compute v hin cy pht sinh
d. Ly kt qu h s tng ng di truyn: Vo file chn DT2.nts, Open v copy bng
h s.
Hnh thc t chc dy hc
- Ging gii ca GV kt hp vi hng dn nguyn l s dng phn tch, so snh cc
trnh t nucleotide v amino acid.
- Tho lu n cc bi t p v cu hoi nho.
Cu hi v bi tp
1. Phn bi t d li u s cp v th cp trong Tin sinh hc?
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2. D li u trnh t nucleotide v amino acid?

3. Mc ch ca vi c phn tch, so snh trnh t nucleotide v trnh t amino acid?
4. S dng phn mm BioEdit so snh hai trnh t nucleotide v hai trnh t
amino acid.
5. S dng BLAST trong NCBI so snh xc inh mc tng ng v trnh t
nucleotide v hai trnh t amino acid.
6. S dng phn mm DNAstar phn tch tnh a dng da trn trnh t
nucleotide v hai trnh t amino acid.
7. S dng NTSYS phn tch tnh a dng di truyn da trn s xut hi n cc on
DNA
Nhim vu cua sinh vin
- Sinh vin c trc bi ging, gio trnh v chun bi cc cu hoi tho lu n.
- Sinh vin hon thnh cc bi t p s dng cc phn mm BioEdit v phn mm
DNAstar.
Hc liu
1. Bi ging ca ging vin;
2. Ti li u hc t p v tham kho:[1] [4] [5].
3. Phong hc c my chiu v ni mng internet
nh gi: Chuyn cn thng qua tham gia d lp, kt qu lm bi t p v tho lu n ca
sinh vin.

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