A Local Improvement Algorithm for Multiple Sequence Alignment
Xiaodong Zhang · OhioLink ETD Center (Ohio Library and Information Network) · 2003
= GB 1Q O: O4 0/ C' *) 5f 3) 5/ 1? Y) Â) b= G-I-0) ,: Ì 37 Ø' *: a ¨+ gA 5-K+ 6; dA 5B : O7 Ù= 3/ 19 5+ ^_ G= @4 0/ P+ Ô' ED : G; Ñ ç2 54 K: O 5B 1+ .fg-I/ 1-I= GB P-K: 9 5/ 1-0? .A ,-0-0+ 69 }= G7 ,9 Ö? .: Of ¬ ,/ P7 5+ 69 ^ 3/ C' *) Ö: OA ,4 U7 5+ ./1Q O) i ¨: O4 K) 5: o: 9 ^= GB C' *+ 64 07 b= @' 0/ P: O7 Õ-0? Y) 5+ 6f Î= R' *: R/ 1f 2 ,B P+ .fg+ .7 8' [= G7 = G2 52 ,4 0: Û / Pf = @' *+ R-K: OB PA ,' 0/ P: O7 ,-j: G; k m & £2 54 0: G 5B P+ 6f -6Ç Þ Â+ FA ,-0+ .9â' *) ,+ F4 *= G7 59 ,: Of -K+ .hiA 5+ .7 ,? .+.-QO+ .7 ,+ .4*= °' *+ .9â 8D ²' 0) 5+ F+ ÔÛ o' *+ 67 5-0/ C_ O+ 6B 1D ²' 0+ .-K'0+ .9â' *: o: OB jH 3: O-K+ ' *: ¬= G7 b= GB CD æ 6+ M' 0) 5+ R= G-lD f g2 ,' 0: G' */ 1? !+ .)b= _ o/ P: O4 à: G; ´: OA 54 N= GB PQ G: O4 0/ C' *) 5f = @7 59 F2 54 *= @? 6' */ 1? = GB 2 54 K: G' *+ 6/ P7 }-K+ .hiA 5+ 67 5? .+; d4 0: Gf ' 0) 5+ ØL Z <è 9 b= @' *= G b= G-K+ s' *: -K' 0A 59 ,D ' 0) 5+ + 6á ¨+ .? Ô' */ C_ O+ .7 ,+ .-0-a:G; I: OA 54 = @B PQ O: O4 K/ 1' 0) 5f : O7 µ' *) 5+ 4 K+ = GB à: O4 0B 19 -0= Gf 2 ,B P+ .-6ÇUH 3+ .-0A,B 1' *-ä-0) ,: Ì 3-à' *) b= @' ; d: O4 !: G' *) 2 54 *= @? 6' */ 1? = GB b2 ,4 0: G' 0+ ./P7 g-0+ 6h iA 5+ .7 5? 6+ .-3=G7 ,9 Î4 *= @7 59 5: Of Q O+ 67 5+ .40= @' *+ 69 -0+ 6h oA ,+ .7 5? 6+ .-. M: OA 54 g) 5+ .A ,4 0A 5-K-0+ .9' *) 5+ TÚ KA 5-l' */ 1e 5? = @' 0/ P: O7 ^: G; q? .: Of gf : G7 5B 1D A 5-0+ 69 Î-0? 6: O4 0+ J-0? Y) ,+ .fg+ G o-0A 5f ÖÒ E: G; cÒ 2 b= G/ 14 0-Ä m , äÈ N-0? 6: O4 0+ <-K?Y) 5+ .fg+ I 3) ,/ P? Y) a/ P-A 5-K+ .9' *: ^+ 6_ @= GB 1A b= @' *+ \' 0) 5+ <h iA b= GB P/ C' ED }: G; T= G7 k m & ÕÇ 5Þ Â+ R; d: OA ,7 59 ' *) 5= @' F; d: O4 }-K/ Pf g2 5B P+ Wf ¬A 5B 1' 0/ P2 5B 1+ W-K+ .hiA 5+ 67 5? .+6-Ä -K) 5: O4 l' *+ .4= _ G+ .4*= @Q O+ ãB P+ .7 ,Q G' *) ë= G7 ,9 ë; d+ Ô N+ 64 7 oA ,f ¬ ¨+ 64 F: G; -0+ 6h iA 5+ .7 5? 6+ .-*ÈÔ b' *) 5+ Rm , Ð-K? .: O4 K+ R/ P-à7 5: G' = ÕQ O: : o9 }f g+ = G-KA 54 0+ M' *: ' 0) 5+ \h iA b= GB 1/ 1' ED g: G; X= G7 k m & Ç bì J: N+ Ô_ O+ .4 6 ; d: O4 34 0+ .=GB P/ 1-K' 0/ P? Rf ¬A 5B C' */ 12 5B P+ \-K+ .hiA 5+ 67 5? .+6-Ä B P: G7 5Q O+ .4J= _ O+ 64 *= GQ G+ B P+ 67 5Q G' 0) bf : G4 0+ <7 iA 5f ¬ !+ .4J: G; U-0+ 6h iA 5+ .7 5? 6+ .-*ÈÔ m , ¹-K? .: O4 K+ Õ4 K+ 6í b+ 6? 6' 0-J' 0) 5+ <? .: O4 K4 0+ .? Ô' M= GB P/ 1Q O7 5f g+ .7 8' Ç & 2 52 ,4 0: _ O+ 69 / 1f / 17 5Q ^L j= G/ & -K-0: o? ./P= @' *+ I U4 0: G; d+ 6-0-K: O4 3: G; [S UB 1+ .? 6' 04 0/ 1? = GB S U7 5Q G/ P7 5+ 6+ .40/ 17 5Q g= G7 59 #L N: Of g2 5A ,' *+ 64 Jm ?./1+ .7 5? 6+ & M? Yß o7 ,: Ì 3B 1+ .95Q Gf + 67 i' 0-` N: GA 5B P9 }B 1/ Pß @+ J' 0: ¬+ ÔÛ 2 54 K+ .-0-fÕD g' 0) b= G7 5ß i-N= G7 59 F= G2 ,2 54 0+ 6? ./c= °' */ P: G7 ' *: = GB PB b' 0) 5+ 2 !+ .: O2 ,B P+ M 3) ,: ¬) 5+ .B 12 ¨+ 69 f g+ N' *) 54 K: OA 5Q O) ,: OA ,' Uf D ¬= G? = @9 5+ .fg/ P? à? = G4 K+ .+.46Ç ` N: OA ,B P9 Ö+ .Yß 8D a' 0: e b7 59 #= G7 s= @9 ,_ o/ P-0: G4 3 3/ C' *) W= g? 6: O7 5-K/ P9 5+ 64 *= G 5B 1+ Õ2 5= @' */ 1+ .7 5? 6+ Õ= @7 59 W' 0: OB P+ 64 *= G7 5? 6+ <: O7 #) 5/ 1-3-K' *A ,9 5+ .7 8' Ç 4 6Ç L j= G/ N= G-<-0: aß o/ 17 59 ' *: Q O/ C_ O+ ^f + ¬' 0) 5+ Ö; d4 0+ 6+ .95: Of ' *: 9 5+ 6_ G+ .B 1: O2 Ùf ÕD s: 37 Ù4 K+ .-K+= G4 K? Y) Â2 b= @' 0) Â= @7 59 ã? .: O4 K4 0+ .? Ô' f D F4 K+ .-K+= G4 K? Y) #9 5/ 14 0+ .? Ô' */ 1: O7 } 3) 5+ .7 ` N= G-3-K' 0A 5? Yß F-0: Of g+ 6 3) ,+ .40+ @Ç ` j= @-}+ .7 5? 6: OA 54 0= GQ O+ .93/ C' *) ) ,+ .B P2 ; dA 5B M9 ,/ P-0? 6A 5-0-K/ P: O7 ,-F= G7 59 ) ,: O-02 5/ C' Y= GB 1/ 1' ED ²; d4 K: Of U4 0: G; îÇ çï GA 5+ .9,+ .-=_ o/ P9 ^; d: O4 ) 5/ P-/ P7 ,2 5A ,' *-U' 0: I' 0) 5/ P-U' *) ,+ .-0/1-.Ç ì J/ P-/ P7 5-K/ PQ O) 8' ä= G7 ,9 Î+ ÔÛ 2 !+ .4K/ P+ .7 ,? .+M à+ .4K+ M/ 17 8_ G= @B PA b= G ,B P+ / P7 ^' *) ,+ ?.: Gf 2 5B 1+ 6' 0/ P: O7 F: G; X' *) ,/ P-j à: O4 0ß Ç `= Gf ×; d: O4 K' 0A 57 b= @' 0+ ¬' *: F) b= _ G+ ) b= @9 Øf ÕD s2 b= G4 K+ .7 8' *-R 3) 5: a+ .9,A 5? = @' 0+ .9Øf + ¬' 0: ¨+ ^= G7 ã) 5: G7 5+ .-l'= @7 59 4 0+ 6-02 !: O7 5-K/ P 5B 1+ \f Î= @7 Ç UV ) 5+ ./14 j-0A ,2 52 ¨: G4 K' 3: G; Xf D Î2 5A 54 0-KA 5/ 1' j: G; X-0? ./1+ .7 5? 6+ </ P-N' 0) 5+ Rf Î= Ú K: O4 j-0: GA 54 0? 6+ \; d: O4 jf g+ ' *: = °' 0' Y= @/ P7 5/ 17 5Q Îf D WQ O: 8=