----???????(Principles of Scoring Matrices)

1
????????
??????????? ----???????(Principles of Scoring
Matrices)

• Blosum??(The Blosum matrices)
• ???????(Matrix Performance)
• ????????,Blosum?????????????????,???PAM????
• ???,???1?250PAM??????,????????Blosum?????????????
  ??????,????????
• Blosum????????????gaps???????,????????????

2
Dotplots - ??????????
???????(The problem with sequence comparison)
??????????????????????????????????????????????,??
????????????? ????????,??????????????????????????
???????????????
3
Dotplots - ??????????
???????(The problem with sequence comparison)
??????????,????????????????,????????????????????
??????????,?????????????????????????
ATGCATGCATGCATGCATATATATATATATATATGCATGCATGCATGCA
TGC

CGATCGATCGATCGATATATATATATGCATATATATGCATGCATGCA
TGCAT
4
Dotplots - ??????????
???????(The problem with sequence comparison)
???????????????????,???????????,????????????,?????
???????,???????????????,???????????????????????,??
???????????(?????????????????)
ATGCATGCATGCATGCATATATATATATATATATGCATGCATGCATGCAT
GC


CGATCGATCGATCGATATATATATATGCATATATATGCATG
CATGCATGCAT
5
Dotplots - ??????????
???????(The problem with sequence comparison)
???,????????????????????,?????????????????????????
?????,????????????????,?????????????????????,?????
??????,????????????????,????????????
ATGCATGCATGCATGCATATATATATAT----ATATATGCATGCATGCAT
GCATGC


CGATCGATCGATCGATATATATATATGCATATA
T----ATGCATGCATGCATGCAT
6
Dotplots - ??????????
???????(The problem with sequence comparison)
?????????(--)?????/???????????????????????????????
,???????????indel???indels???????????????????
?????gaps???,??gaps????????????????
----AT--GCAT--GCATGC--ATGCATATATATATAT----ATATAT--
--GCATGCATGCATGCATGC



CGATCG--ATCG--AT--CG--------ATATATATATATGCATATAT
ATGCATGCATGCATGCAT
7
Dotplots - ??????????
???????(The problem with sequence comparison)
??,???gaps??????????????????????????,?????????
gaps??????,????????????????????gaps,???????????
????(????,???)??????,?????????????????????,??????
?????????????? ???????????,indel????????????????
??????,??????,????indels????????????????,???????
?,gaps?????????????????indels(gaps)???????????

8
Dotplots - ??????????
???????(The problem with sequence comparison)
???,?????????(shift),?????????gaps??????????????
,????????????????????????????,?????????????,??????
????
ATGCATGCATGCATGCATATATATATATATATATGCATGCATGCATGCAT
GC CGATCGATCGATCGATATATATATATGCATATATATGCATGCATGC
ATGCAT
9
Dotplots - ??????????
???????(The problem with sequence comparison)
ATGCATGCATGCATGCATATATATATATATATATGCATGCATGCATGCAT
GC CGATCGATCGATCGATATATATATATGCATATATATGCATGCATGC
ATGCAT
??,?????????(motif)??????,????????????????????????
??????????????????????????,?????????????????,?????
?????????????,???????????
10
Dotplots - ??????????
???????(The problem with sequence comparison)
??,?????????????????????,?????????????? ?????
?????,?????,?????????gaps?????,????????????????,??
???????????,??????????????????????????,??5??3???
?
ATGCGACATTATATGGACGCCGACAATATGCATGACTAGCATAGCATGCG
AT
TAGCGTACGAGACGTTCAGTAGGTATAACAGTCGCAGGTATCTTAC
AGCGTA
11
Dotplots - ??????????
???????(The problem with sequence comparison)
ATGCGACATTATATGGACGCCGACAATATGCATGACTAGCATAGCATGCG
AT
ATGCGACATTCTATGGACGCTGACAATATGGATGACTTG
CAGAGCATGCGAT
???,??????????????,?????????
ATGCGATCAGATGATCAGATGACATGACATAGGCATACCCAATTGACATA
CG
CGTATGTCAATTGGGTATGCCTAT GTCATGTCAT
CTGATCATCTGATCGCAT
12
Dotplots - ??????????
???????(The problem with sequence comparison)
ATGCGATCAGATGATCAGATGACATGACATAGGCATACCCAATTGACATA
CG
CGTATGTCAATTGGGTATGCCTAT GTCATGTCAT
CTGATCATCTGATCGCAT
??,??????????????????,??????????????????,?????????
,?????????????????????????????????????????????
13
Dotplots - ??????????
?????????
????????????????????????,????????????,????????????
,???????????????????????????????????,????????????
??????????????????,??????????????
14
Dotplots - ??????????
?????????
??,?????????????,???????????????????????,?????????
??????????????????????????????????????????,?PAM?BL
OSUM?BLOSUM32?,???????????????????????????????????
?????????
15
Dotplots - ??????????
?????????
??,?????????????????????,?????????????????????????
???????,???????????????????????,??????????????????
???????
16
Dotplots - ??????????
?????????
C X G X A
T G C T X
A X A T G C
--------------- A T G C
17
Dotplots - ??????????
?????????
??????????????????????????????????????????????????
???????????
18
Dotplots - ??????????
?????????
A X . C . X
A T G C A GX . X
T . X
G A T G C A . X ---------------------
- G A T G C
19
Dotplots - ??????????
?????????
??,????????????????????,??????????????????????????
????????????????????????????,?????????
20
Dotplots - ??????????
?????????
????????????????,?????????????????
A X T X C G T A
G X C X A
T G C -------------------- A T G
C
21
Dotplots - ??????????
?????????
??????,?????????????????????????????????????????
????????????????????????????????45????
22
Dotplots - ??????????
?????????
?????????????????????????????,???????????????????,
??????????????????
23
Dotplots - ??????????
?????????
24
Dotplots - ??????????
?????????
??????????stem-loops?,?????????????????
25
Dotplots - ??????????
?????????
??????????????????????,?gaps??????????????????????
???,??????gaps?????????????,??????????????????????
gaps,??????????gaps????????,??????????????????????
???????????gaps??????gaps??,???????,???????gap,???
gap???,???????
26
Dotplots - ??????????
?????????
??????????gaps,???????indel?????????,???????????
Gaps??????????????? ???????,??????????????????????
??????gaps,??????gap?????????????,????????????????
(non-overlapping)??????????gaps?????????
27
Dotplots - ??????????
?????????
28
Dotplots - ??????????
?????????
??,??????????????????????????,????????????????????
??????????????????????????????,???????,??????????
???????,??????????(??????????????????)?
29
Dotplots - ??????????
?????????

• ??,????????????
• ????,?????????????,?????????????????????
• ???????????,??????????,????????

30
Dotplots - ??????????
?????????
??????????????????????,??,????????????????????,???
??????????
31
(No Transcript)
32
Dotplots - ??????????
?????????
????????????????(?100??)????????????,?????????????
?????????????????????,???????????????,????????????
?????
33
Dotplots - ??????????
?????????
????????????????(?100??)????????????,?????????????
?????????????????????,???????????????,????????????
????? ?????????????????????(word)???????????????
???????,?????????,????????????????,??,??????????
???
34
Dotplots - ??????????
?????????
??????????????????????,??????????,????????????????
???????????????,???10??????,?????????????,?????wi
ndow(??)???????????????????,?????????????????????
?????????????window??????????,??????????????????
????????????,?????????????(stringency)??????????
??,?????,?????????????
35
Dotplots - ??????????
?????????
?????window???21,????14?????,??????????21??,??????
???14?????????????,????window?????????????????????
?????,?????????????????????window????????????,????
?,???????????window???????
36
(No Transcript)
37
Dotplots - ??????????
?????????
???,??? ???window??stringency?????????????????,?
?????????,?????????????,??????????????????
38
Dotplots - ??????????
?????????
??????????????????????,???????????,????????,??????
?????????????????????,?????????,???????????????
?????????,????????????? ???????????????,??????????
?????????????
39
???????--Globally optimal sequence alignment
The Needleman-Wunsch-Sellers Algorithm (Dynamic
programming)

• Contents of this section
• Dynamic Programming
• The Needleman-Wunsch-Sellers Algorithm
• An explicit example
• Gap penalties
• Literature and further reading

40
???????--Globally optimal sequence alignment
The Needleman-Wunsch-Sellers Algorithm (Dynamic
programming)
????(Dynamic Programming)