ks1, s2, ... ,skk2

1SPSum-of-Pairs

k k

c1,c2,,ckkpSPsum-of-pairs p(1,2)p (1,3)...p(1,8)p (2,3)p(2,4)... p (2,8)...p (7,8) -7-6-5-4-3-2-1+2 = -26

SP

ijs i s j

2

2k - 1

kA

a[ 0, 0, ,0 ] = 0

a[ i ] = max {a[ i - b ] + SP-score(Column(s, i, b))} (3-37)(3-38) if bj = 1if bj = 0

3.17 O(2ki=1,...,k si) O(2kNk)

3

stijij 0:s:i 0:t:j i:s:mj:t:nS:t: ji

AB a[i, j] = sim(0:s:i , 0:t:j)b[i, j] = sim(i:s:m , j:t:n)

A BB00

ABC=A+BijCAB

C

-ATTCGGGATTC-- c abca b

3-1s1, s2, ... ,skSP-score() L score(ij) Lij Lij = L - ( sim(sx, sy) ) x

4

siscOkn2

scs1s2

sk

(sc, s1) (sc, s2) (sc, sk)

sim( si, sc )

5 s1 = ATTGCCATT s2 = ATGGCCATT s3 = ATCCAATTTT s4 = ATCTTCTT s5 = ACTGACCsc=s1ATTGCCATT ATTGCCATT-- ATTGCCATT ATTGCCATTATGGCCATT ATC-CAATTTT ATCTTC-TT ACTGACC-- ATTGCCATT--ATGGCCATT-- ATC-CAATTTT ATCTTC-TT-- ACTGACC----

3.1 1ijk,ij, dc(si, sj) D(si, sc) + D(sc, sj) 3-433.2 3-44

5k k

CTCGCTxyz8

a=bp(a,b)=1 p(a,b)=0p(a,-)=-1 CTCGCT

Alignment of alignments, AA

121s1s2si2t1t2tjs1s2sit1t2tj=s1t112

11s1s1a1a2als1ls1s122t1t1b1b2blt1lt1t13a1a2als1b1b2blt1412-

1: s1 -H-LVV 2: t1 L-HCLV s1 -H-LVV s2 G-VLVC t2 VLHCL- t1 LHCLV- s3 GN-LVV

AA--H--LVV-G--VLVG-GN--LVVL-HC-LV-V-HC-L

1245HLVVGVLVGGNLVVLHCLV-VHCL--

n

1

2AA

32n s1 s2 s3 s412

6

12 3

((LYCES, SPIOL 84), (YEAST, (XENLA,(((RAT, MOUSE 96), HUMAN 83), CHICK71) 66), DROVI 58))

ClustalW ClustalW

EBICLUSTALW http://www.ebi.ac.uk/clustalw/

7

HLVVGVLVGGNLVVLHCLV-VHCL-- 1ATNTSC (N - A,T,C,G ; S - G,C)

2Profile

P=(P1,P2,,PL)P

Pj=(pj0,pj1,,pj|A|)

APjkAk j 0-

ATTATAACTTCTTATACTTTAGAAT 1 2 3 4 5 () A 0.8 0.2 0.2 0.6 0.0 T 0.0 0.4 0.6 0.4 1.0 C 0.2 0.2 0.2 0.0 0.0 G 0.0 0.2 0.0 0.0 0.0

s=a1a2amaj

|A|AAkAkA0-s