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1 22 JSBi -1-
2
3 / AB AB 1 A B 2 B AB 3 A B AB 4 O A B AB -3-
4 6 A a AA aa 1 A a 2 Aa 3 AA RNA 2 3 TATA 4 RNA mrna UTR -4-
5 8 RNA (a) (d) (a) DNA (b) (c) RNA (c) (d) 1 (a) (b) mrna (c) (d) mrna 2 (a) (b) mrna (c) (d) mrna 3 (a) (b) trna (c) (d) 4 (a) (b) mrna (c) (d) trna -5-
6 10 RNA mrna mrna RNA RNA
7 N N- 2 3 O O G GTP 3 4 Na + K ras myc 2 Rb p
8 SNP DNA 2-8-
9 15 DNA 1 a, c 2 a, d 3 b, c 4 b, d 5-9-
10 16 LINE SINE 1 10% 2 30% 3 50% 4 70% 17 A B DNA PCR (a) A DNA B 5 -GAGTCAACGGATTTGGTCGT CGAGATCCCTCCAAAATCAA-3 3 -CTCAGTTGCCTAAACCAGCA GCTCTAGGGAGGTTTTAGTT-5 (a) 5 -GAGTCAACGGATTTGGTCGT CGAGATCCCTCCAAAATCAA GCTCTAGGGAGGTTTTAGTT AACTAAAACCTCCCTAGAGC TTGATTTTGGAGGGATCTCG-3-10-
11 18 SDS SDS-PAGE SDS-PAGE (a) (b) 1 (a) (b) 2 (a) (b) 3 (a) (b) 4 (a) (b)
12 20 X (AND) 2 110(2) AND 101(2) = 100(2) (n) n 6(10) = 110(2) x f(x) f(x) = x AND 101 (2) y, z f(y) = f(z) 1 y = 110(2) z = 100(2) 2 y = 101(2) z = 100(2) 3 y = 011(2) z = 101(2) 4 y = 000(2) z = 101(2) -12-
13 22 1 Perl 2 Ruby MySQL 3 JIT CISC (Complex Instruction Set Computer) RISC(Reduced Instruction Set Computer) CPU -13-
14 24 ( a ) ( d ) ( a ) ( b ) ( c ) ( d ) 1 (a) scp (b) ssh (c) telnet (d) ftp 2 (a) ftp (b) sftp (c) telnet (d) ssh 3 (a) telnet (b) ftp (c) scp (d) ssh 4 (a) telnet (b) ssh (c) ftp (d) sftp 25 O(n 2 ) 1 n 2 2 n 2 3 n > c n a n 2 a c 4 n > c n a n 2 a c -14-
15 26 ( a ) ( c ) ( a ) O(n 2 ) O(n log n) ( b ) O(n log n) ( c ) 1 (a) (b) (c) 2 (a) (b) (c) 3 (a) (b) (c) 4 (a) (b) (c) 27 AB * * A AB * * B AB * * 1 AA * B * * 2 AB * A * * 3 AB * B * * 4 AB * C * * -15-
16 28 2 S0, S1 S0 0 1 S0 S1 0 S1 S0 1 S0 S S S1 3 0 S0 4 1 S1 29 (index) 1 2 B- 3 B- 4 B
17 h(x) a, b h(a)+h(b) = h(a+b) 4-17-
18 31 SQL SELECT FROM WHERE = H1N1 AND > 1976 ; AAD17229 Human HA H1N1 USA 1918 ABD95350 Human HA H1N1 Russia 1977 ACF54400 Human HA H3N2 Hong Kong 1968 ACP41105 Human HA H1N1 USA 2009 ACU79959 Human HA H2N2 Japan 1957 AAF75994 Swine HA H1N2 USA 1999 AAB39851 Swine HA H1N1 USA 1976 AAD25304 Avian HA H1N1 Canada 1976 AAT65329 Avian HA H1N1 Canada
19 32 XML (extensible Markup Language) 1 XML 2 XML 3 XML 4 XML XML XML , 3, 3, 8, 9,
20 34 2 X, Y Pr(A, B ) A B E(A ) A Var(A ) A 1 X, Y XY E(XY ) E(X )E(Y ) 2 X, Y X, Y Pr(X, Y ) Pr(X )Pr(Y ) 3 X Var(X ) X X 2 Var(X ) = E(X 2 ) (E(X )) 2 4 Y X Pr(X Y ) Pr(X,Y )/Pr(Y ) 35 X Y N(0,1) N(0,1) X Y 1 X Y 2 X + Y 3 X + Y 2 4 2X 4-20-
21 p(x) p(x) < 0 x K- (K-means method) 2 UPGMA (Unweighted Pair Group Method with Arithmetic mean) 3 (Self-Organizing Map) 4 Fuzzy C-means -21-
22 38 10 X1, X2,, X y1, y2,,y10 X k- d(x, Xi ) 10 yi 10 d(x, Xi ) k- k- k k=1 k=3 2 k=1 k=3 3 k=1 k=3 4 k=1 k= n-fold 1/ n 2 n-fold n n = 2 3 LOO (leave-one-out)
23 40 TP = True Positive TN = True Negative FP = False Positive FN = False Negative 1 (recall) TP / (TP + FN) 2 (precision) TP / (TP + FP) 3 F (F-measure) 2TP / (TP+FN+TP+FP) 4 41 BLAST 1 DNA DNA 2 DNA 3 (low-complexity) (% identity) 4 PSI-BLAST (position-specific scoring matrix; PSSM) -23-
24 42 A B A B 1 B A 2 A B 3 B 4 A 43 ClustalW (progressive method)
25 44 BLAST (bit score) 1 BLOSUM45 BLOSUM s 10 S 45 BLAST = 0 Seq1 Seq2 GAGCAGCTAGATCGGATTGTTAGA CATGTGATAGACCGTATTAATGCA
26 46 Gene Ontology (GO term) A is_a B A B A part_of B A B A B GO term A is_a B A part_of B A B mitochondrion is_a cytoplasmic part A is_a B B is_a C A is_a C A part_of B B part_of C A part_of C A is_a B B part_of C A part_of C A part_of B B is_a C A part_of C 1 cytoplasmic part is_a intracellular part 2 cytoplasmic part part_of intracellular part 3 mitochondrion is_a organelle 4 intracellular organelle is_a intracellular -26-
27 47 RNA 1.((((...((.(((...)))))..)))). 2.((((..(((((((...))))))))))). 3 (((((..(((((((...)))))))))))) 4.(((...((..((...))))...))). -27-
28 48 A E A B C D E PAM BLOSUM PAM20 PAM70 PAM70 1 A B 2 B C 3 C D 4 D E 49 4 DNA position 1 position 2 position 3 position 4 A T G C GAGGTCT 1 AGGT 2 GAGG 3 GTCT 4 GGTC -28-
29 50 5 DNA 4 fj(a) j a p(a) a p(a) = p(t) = p(g) = p(c) = 0.25 = T A T A T 2 T A T T T 3 T A A G T 4 T A A C T 5 j f j (a) log 2 j =1 a {A,T,G,C} f (a) p(a)
30 51 C-X-X-C-x(5,7)-C-[FWY]-[LIV]-C X (-) ([ ]) 1 x(m,n) m n 1 CTGCGGCFVC 2 CTICGGENNRTCFVC 3 CLIHGGENDRTCWVC 4 CTMCGGEHNNRTCFVC 52 DNA (palindrome) DNA 1 5'-ATGGGCCGGCCCAT-3' 3'-TACCCGGCCGGGTA-5' 2 5'-ATGGGCCTTTAAAG-3' 3'-TACCCGGAAATTTC-5' 3 5'-ATGGGCCCCGGGTA-3' 3'-TACCCGGGGCCCAT-5' 4 5'-ATGGGCCATGGGCC-3' 3'-TACCCGGTACCCGG-5' -30-
31 53 (cis) (trans) C
32 55 2 L- D- L- Cα N C Cβ CαN CαC CαCβ L- 1 (CαN CαC) CαCβ > 0 2 (CαN CαC) CαCβ = 0 3 (CαN CαC) CαCβ < 0 4 (CαN CαC) CαCβ = Molecular Dynamics MD 2 Molecular Mechanics MM
33 57 PDB(Protein Data Bank) -33-
34 β 3 X TIM (Rossman) SCOP CATH 3 SCOP all all /
35 PDB(Protein Data Bank) BLAST 1 2 ab initio
36 62 5 A1~A5 B1~B5 2 C C RMSD(Root Mean Square Deviation) A1 B1 3.0 A2 B2 1.0 A3 B3 0.0 A4 B4 1.0 A5 B
37 63 DNA 1 B 2 (major groove)- (minor groove)
38 64 1 SCOP (space filling model) CNV 2 QTL 3 SNP 4 VNTR -38-
39 66 ABO 3 A B O AA AO BB BO AB OO 6 A A B B AB O A B AB O A B O 1 A 0.3 B 0.2 O A 0.1 B 0.5 O A 0.1 B 0.4 O A 0.3 B 0.3 O
40
41
42 70 (a) (b) (a) ML OTU Operational Taxonomic Unit; OTU 4 3 OTU 5 (b) OTU (a) NJ (b) 15 2 (a) NJ (b) 21 3 (a) MP (b) 15 4 (a) MP (b)
43 71 (Newick format) 1 ((a,b), c, (d, (e, f))) 2 (((a,b),c), d, (e,f)) 3 ((a, b), (c, d), (e, f)) 4 (c, ((e, f), d), (b, a)) -43-
44 72 (a) (b) (c) n x / d d p = ( 3/ 4) ( 3/ 4)e ( 4 d /3) L(d; x) (a) n! d x!(n x)! (a) (d; x) (b) d d (c) 1 (a) p x (1 p) (n x) (b) d (d; x) dd = 0 (c) 3 4 log x n 2 (a) p x (1 p) (n x) (b) d2 (d; x) = 0 dd 2 (c) 4 3 log x n 3 (a) ( 3/ 4) ( 3/ 4)e ( 4 d /3) (b) d (d; x) dd 4 (a) ( 3/ 4) ( 3/ 4)e ( 4 d /3) (b) d2 (d; x) = 0 (c) 3 4 log x n = 0 dd 2 (c) 4 3 log x n -44-
45 mrna 2 3 mrna 4-45-
46 75 A B X B A PCR X B Ct A Ct 2 1 X A B 2 2 X A B 4 3 X B A 2 4 X B A 4 76 X A B A B 1 2 X 2 2 X 3 2 X mrna 4 2 X -46-
47 77 v Y [Y] v = k K K +[Y] k K 1 v k 2 [Y] K 3 [Y] K v 4 Y 78 X k (>0) X 4 X -47-
48 79 y1, y2 1 1, 2 2 1, 2 3 1, 2 4 1, 2-48-
49 80 X Y Z Sx Z Z Sx Y Z -49-
50 22 JSBi
51 -51-
( )/2 hara/lectures/lectures-j.html 2, {H} {T } S = {H, T } {(H, H), (H, T )} {(H, T ), (T, T )} {(H, H), (T, T )} {1
( )/2 http://www2.math.kyushu-u.ac.jp/ hara/lectures/lectures-j.html 1 2011 ( )/2 2 2011 4 1 2 1.1 1 2 1 2 3 4 5 1.1.1 sample space S S = {H, T } H T T H S = {(H, H), (H, T ), (T, H), (T, T )} (T, H) S
More informationA(6, 13) B(1, 1) 65 y C 2 A(2, 1) B( 3, 2) C 66 x + 2y 1 = 0 2 A(1, 1) B(3, 0) P 67 3 A(3, 3) B(1, 2) C(4, 0) (1) ABC G (2) 3 A B C P 6
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