1 81 multiple sequence alignment

... full-length protein sequences The performance of programs that are based 12 0097 65 Bb 31 Ca Da EVX 12 10 334 81 13 12 11 10 65 12 5385 11 2097 Figure a DIALIGN run on the Hox sequences from Figure ... processors and Gbyte of RAM anchor alignment length aligned sequences none genes BLASTZ hits 2 817 59 252346 239326 668 10 91 113 9 244 19 5 33 score 4:22:07 1: 18 :12 0 :19 :32 11 66 10 07 742 2958 3674 4036 CPU ... local alignments of all input sequences using BLASTZ [42] with non-stringent Alignment scores Ref3 283,273 283 ,13 6 0.999 4/23 Ref4 Ref5 Total 36, 515 36, 611 1. 002 6 /16 29, 214 29,257 1. 0 01 4 /12 6 71, 624...

Ngày tải lên: 12/08/2014, 17:20

... PROBCONSRNA 1. 10 74.39 29.60-69.950 00.00-00.00-05.63- 21. 45-40.28 -14 .18 -00.73 69.03 28.63-68 .19 0 00.00-00 .18 -07.32 -11 .93- 41. 99 -16 .18 -00.05 71. 57 35. 51- 71. 250 02 .19 -04. 01- 04 .12 -16 .02-45.77 -19 .62- 01. 34 ... PROBCONSRNA 1. 10 94.38 64.00-92. 610 6.79 -14 . 71- 32.03-52.40-92.420 48 .17 -13 .00 92.85 61. 22- 91. 1008.27 -18 .88-27.40-48. 81- 84 .15 -54.40 -12 .94 95.44 64.96-94.6 218 . 51- 32.08-28.78-49.77-87. 915 6.57-20.28 ... 00.00-34.84-50.9937. 81- 45.7004.65-36.77 77.36 75. 810 73.3200.00-40.87 -16 .95-39.54-52.37-06.87-43.47 70.30 70.400 65.3400 .11 -43.62 -11 .79-32.79-43 .11 -14 .80- 41. 89 72.23 70.440 69.5002.86-49.56 -10 .18 -38.75-54.82 -19 .65-43.56...

Ngày tải lên: 12/08/2014, 17:20

... cox1 cox2 cox3 cytb nd1 nd2 nd3 nd4 nd4l nd5 nd6 684 17 1 15 36 672 786 11 31 942 10 32 345 13 71 288 18 03 540 42 88 34 45 74 44 63 11 65 16 10 3 25 405 10 8 10 08 443 516 676 589 626 222 8 31 183 10 40 ... 3:7 650 600 550 500 2000 19 00 18 00 17 00 16 00 15 00 14 00 13 00 12 00 11 00 10 00 singleton site 450 400 350 900 800 700 600 500 400 300 200 10 0 constant site 300 250 200 15 0 10 0 50 missing data http://www.almob.org/content/3 /1/ 7 ... 3:7 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 Landan G, Graur D: Heads or tails: a simple reliability check for multiple sequence alignments Mol Biol Evol 2007, 24 :13 80 -13 83 Björklund...

Ngày tải lên: 12/08/2014, 17:20

... s1 & s ] = Pr[E 2,int (s 1) ∧ E1,int (s ) | s1 & s ] = Pr[E 2,int (s 1) | E1,int (s ), s1 & s ] × Pr[E1,int (s ) | s1 & s ] Eq.(9) = Pr[s | s1] × Pr[E1,int (s ) | s1 & s ] Intuitively, Pr[e1,int(σ2)|s1&s2] ... (13 ) s′ 1 2 Pr[s ∪ s ∪ s int | s1 & s ] 2 = Pr[E int (s ∪ s ) ∧ E1,2(s int ) | s1 & s ] s′ = Pr[E1,2(s int ) | E int (s ∪ s ), s1 & s ] × Pr[E int (s ∪ s ) | s1 × s ] s′ int int Eq .11 ) = Pr[E1,2(s ... C, 18 70, Denmark and 2Bioinformatics Group, University of Freiburg, Georges-Köhler-Allee 10 6, Freiburg, 7 911 0, Germany Received: 10 April 2 010 Accepted: 21 May 2 010 Published: 21 May 2 010 © 2 010 ...

Ngày tải lên: 12/08/2014, 17:20

... the sequences are S1 = S1 ,1 S1,2 · · · S1,|S1 | S2 = S2 ,1 S2,2 · · · S2,|S2 | ··· Sk = Sk ,1 Sk,2 · · · Sk,|Sk | , then the multiple alignment will be S1 = S1 ,1 S1,2 · · · S1,|A | S2 = S2 ,1 S2,2 ... IAVEWESNG Figure 1. 1: A sample of multiple sequence alignment Figure 1. 1 is a sample of multiple sequence alignment which aligns different protein sequences together In an alignment, we normally ... Introduction 1. 1 Basic Concept of Sequence Alignment 1. 2 Pairwise Sequence Alignment Method 1. 2 .1 Dynamic Programming Method 1. 2.2 Global Alignment...

Ngày tải lên: 26/09/2015, 09:48

... multiple sequence alignments BMC Bioinformatics 2008, 9 :15 1 Guerrero et al Algorithms for Molecular Biology 2 010 , 5:24 http://www.almob.org/content/5 /1/ 24 10 11 12 13 14 15 16 17 18 19 20 21 22 ... identity GS1 Plant Arabidopsis thaliana GS1 Plant Arabidopsis thaliana AtGS1 isoform AF 419 608 tity AtGS1 isoform AY0 911 01 GS1 Plant GS1 GS1 Plant Plant Arabidopsis thaliana AtGS1 isoform AY088 312 Arabidopsis ... isoform AK243037 Q10DZ8 GS1 Plant Oryza sativa OsGS1 isoform AB180689 Q10PS4 MDH -1 Mammalian Mus musculus MmMDHm NM_008 618 NP_032644 MDH -1 Mammalian Sus scofra ScMDHm MN_ 213 874 MDH -1 MDH -1 Mammalian...

Ngày tải lên: 20/12/2015, 08:16

... Ethernet (E1) 16 00 Ethernet (E0) Ethernet (E1) Serial (S0) Serial (S1) 17 00 FastEthernet (FA0) FastEthernet (FA1) Serial (S0) Serial (S1) 2500 Ethernet (E0) Ethernet (E1) Serial (S0) Serial (S1) 2600 ... Basics v 3.0 - Lab 10 .1. 6 Copyright  2003, Cisco Systems, Inc Router Interface Summary Router Ethernet Ethernet Serial Serial Interface Model Interface #1 Interface #2 Interface #1 Interface #2 ... Ethernet (E1) Serial (S0) Serial (S1) 2600 FastEthernet 0/0 FastEthernet 0 /1 (FA0 /1) Serial 0/0 (S0/0) Serial 0 /1 (FA0/0) (S0 /1) In order to find out exactly how the router is configured, look at...

Ngày tải lên: 11/12/2013, 14:15

... Ethernet (E1) 16 00 Ethernet (E0) Ethernet (E1) Serial (S0) Serial (S1) 17 00 FastEthernet (FA0) FastEthernet (FA1) Serial (S0) Serial (S1) 2500 Ethernet (E0) Ethernet (E1) Serial (S0) Serial (S1) 2600 ... Basics v 3.0 - Lab 10 .1. 6 Copyright  2003, Cisco Systems, Inc Router Interface Summary Router Ethernet Ethernet Serial Serial Interface Model Interface #1 Interface #2 Interface #1 Interface #2 ... Ethernet (E1) Serial (S0) Serial (S1) 2600 FastEthernet 0/0 FastEthernet 0 /1 (FA0 /1) Serial 0/0 (S0/0) Serial 0 /1 (FA0/0) (S0 /1) In order to find out exactly how the router is configured, look at...

Ngày tải lên: 11/12/2013, 14:15

... Phase Phase 1+ 2 Phase 1+ 2+3 Phase 1+ 2+3+3.f Recall 94.08% 34.99% 89.90% 53.90% 88.82% 73.44% 88.80% 74.83% F-Measure 51. 00% 67.40% 80.40% 81. 22% Table 1: YAWA evaluation Figure 3: Alignment after ... Computational Linguistics, 19 (2): 263– 311 Thomas G Dietterich 19 98 Approximate Statistical Tests for Comparing Supervised Classification Learning Algorithms Neural Computation, 10 (7) 18 95 -19 24 Rong-en Fan, ... Aligner Precision Recall YAWA MEBA COWAL 88.80% 92.05% 86.99% 74.83% 71. 00% 79. 91% F-measure 81. 22% 80 .17 % 83.30% Table 3: Combined alignment Conclusions and further work Neither YAWA nor MEBA needs...

Ngày tải lên: 08/03/2014, 21:20

... F Y W 12 -2 -3 -2 -3 -4 -5 -5 -5 -3 -4 -5 -5 -2 -6 -2 -4 -8 C 1 1 0 -1 -1 0 -2 -1 -3 -1 -3 -3 -2 S 0 0 -1 -1 -1 -1 -2 -3 -3 -5 T -1 -1 -1 -1 0 -1 -2 -2 -3 -1 -5 -5 -6 P 0 0 -1 -2 -1 -1 -1 -2 -5 ... -3 -1 -1 -3 -2 -2 E -2 -4 -4 -2 -3 -3 -2 -2 -2 -3 -3 G -3 -3 -1 -2 -1 -2 -1 -2 -2 -3 H -3 -3 -2 -1 -3 -1 I -2 -3 -2 -1 -2 -1 L -1 -3 -1 -1 -3 -2 -2 K -2 -1 -1 -1 -1 M -4 -2 -2 -1 F -1 -1 -4 -3 ... -1 -3 -2 -1 -1 -3 -2 -3 R -3 0 -3 -3 -2 -3 -2 -4 -2 -3 N -3 -1 -1 -3 -4 -1 -3 -3 -1 -1 -4 -3 -3 D -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 C -2 -3 -2 -3 -1 -1 -2 -1 -2 Q -2 -3 -3 -2 -3 -1...

Ngày tải lên: 16/03/2014, 02:20

... target tree sequence covering s([i1,i2]) as a non-contiguous tree sequence pair 9: Insert them into p[j1, j2] 10 : end if 11 :end 12 : foreach target span [i1,i2], 13 : find a source span [j1, j2] with ... each source tree sequence covering s([j1, j2]) with each target tree sequence covering [i1,i2] as a non-contiguous tree sequence pair 17 : Insert them into p[j1, j2] 18 : end if 19 : end SncTSSG ... aligned to [i1,i2] 14 : if any source word in [j1, j2] is aligned with target words outside [i1,i2], then 15 : create sub-span set s([j1, j2]) to cover all the source words aligned to [i1,i2] 16 : Pair...

Ngày tải lên: 17/03/2014, 01:20

... f1J ) and T (e1I ) , the tree sequence- to-tree sequence translation model is formulated as: Pr (e1I | f1J ) = ∑ Pr (e1I , T (e1I ), T ( f1J ) | f1J ) T ( f1J ),T ( e1I ) = T( ∑ f1J ),T I ( e1 ... f1J ),T I ( e1 ( Pr (T ( f1J ) | f1J ) ) ⋅ Pr (T (e1I ) | T ( f1J ), f1J ) ⋅ Pr (e1I | T (e1I ), T ( f1J ), f1J )) In our implementation, we have: (1) 1) Pr (T ( f1J ) | f1J ) ≡ since we only use ... sequences r =< TS ( f j1j2 ) , TS (eii12 ) , A >, where: T ( f1J ) A T (e1I ) TS ( f j1j2 ) is a source tree sequence, covering the span [ j1 , j2 ] in T ( f1J ) , and Figure 1: A word-aligned parse...

Ngày tải lên: 17/03/2014, 02:20

... 4 61 26 38 14 43 33 15 0 10 13 11 12 32 26 13 11 11 14 7 15 1 55 22 14 6 53 17 24 16 19 21 12 62 32 267 16 22 20 18 90 8 17 16 10 7 98 95 38 11 83 35 17 11 12 12 42 17 14 3 14 12 50 0 4 12 10 56 61 ... sno _14 q I_II SRP_bact SRP_euk_arch S_box T-box TAR THI tRNA U1 U2 U6 UnaL2 yybP-ykoY 11 62 76 18 8 48 65 49 16 7 53 12 6 98 51 45 84 733 786 18 8 18 1 764 18 1 12 4 80 89 11 4 44 11 4 12 2 91 18 286 3 21 2039 ... 286 3 21 2039 82 11 2 30 13 8 12 7 568 45 61 32 38 31 67 32 99 63 33 29 59 408 464 12 4 82 403 11 7 40 48 57 67 14 76 94 51 165 14 4 10 12 65 83 21 71 64 288 17 15 19 20 17 22 52 36 19 18 27 227 246 76...

Ngày tải lên: 12/08/2014, 17:20

...  (18 ) 10 4 extra λ2 8 .15 60 ± 12 .485% 6 .17 11 ± 12 .907% 5.0458 ± 13 .280% 4.3056 ± 13 .627% 3.2047 ± 14 .437% 2.5806 ± 15 . 214 % 2 .17 01 ± 15 .984% 1. 8758 ± 16 .758% 1. 6525 ± 17 .544% 1. 4762 ± 18 .347% 1. 0250 ... as an additional CSV-file [see additional file 1] 10 BLOSUM62 L = 250 α =10 β =1 α =12 β =1 α =14 β =1 α =16 β =1 gapless Gumbel -20 P(s*) 10 10 -40 0 .15 0 .10 All estimated standard errors in this paper ... case for not too small p-values 10 10 10 10 BLOSUM62 (12 ,1) -14 BLOSUM62 gapless Gumbel modified Gumbel -20 L=40 10 0 .16 -40 0 .12 0.08 10 0.04 -60 0.00 0 10 0 L=400 20 10 200 300 400 500 s* Figure...

Ngày tải lên: 12/08/2014, 17:20

... 33.3 31. 8 34 .1 PF00486 9 615 75 30 - 34 69 10 7 950 55 52 10 4 63.9 92.8 64.9 89.7 PF005 71 95 51 119 19 - 73 14 3 268 19 93 54 50 15 2 6 .15 3.08 1. 54 1. 54 PF00097 9423 41 33 - 18 38 94 517 44 43 11 5 53.2 ... (1) (2) (3) (4) PF 013 81 9993 53 23 - 25 55 13 6 764 57 55 17 5 13 .3 26.7 25.3 34.7 PF00006 9796 209 43 - 13 4 248 280 4364 48 49 88 42.8 36.6 36.6 38.0 PF00989 96 81 95 17 - 43 88 19 7 12 81 50 51 159 ... PF0 014 9 9072 19 8 14 - 13 3 256 552 3 515 47 46 17 2 75.4 71. 9 72.3 76 .1 Average 9503 95 27 53 10 4 19 5 15 33 49 48 13 1 47.0 48.9 48.5 52.8 The ten biggest Pfam entries containing 9,000 -10 ,000 sequences,...

Ngày tải lên: 12/08/2014, 17:20

... 4, 8, 16 and 32 graphs Method/Number of graphs 16 32 Score -4098 -11 827 -568 61 -267004 Time 22 53 313 13 33 Score -10 99.6 -2688 .1 -10 268.3 -82250 Greedy GAVEO ACOMGA2 Time 756 18 04 715 5 16 378 ... REFERENCES [1] [2] [3] [4] [5] [6] [7] [8] [9] [10 ] [11 ] -2997 -2627 -16 42 -14 39 -12 00 -11 31 Fig.2 Comparison of results of ACO-MGA2 algorithm and GAVEO algorithm with data set of 16 graphs when ... “Evolutionary Construction of Multiple Graph Alignments for the Structural Analysis of Biomolecules,” Bioinformatics vol 25, No .16 , 211 0- 211 7 J F Gibrat, T Madej and S H Bryant (19 96), “Surprising similarities...

Ngày tải lên: 14/10/2015, 15:23

... Total 200 (13 ) 10 50 (44) 12 50 (57) 12 25 (12 ) 375 (18 ) 17 5 (30) 14 25 (25) 14 25 (62) 14 25 (87) 225 (22) 10 27 (28) 12 52 (48) 12 00 (16 ) 398 ( 21) 17 3 (35) 14 25 (38) 14 25 (38) 14 25 (83) Page of 14 (page ... prediction AIDS Res Hum Retroviruses 2003, 19 :14 5 -14 9 Page 13 of 14 (page number not for citation purposes) Retrovirology 2008, 5 :11 0 10 11 12 13 14 15 16 17 18 19 20 21 22 23 Richman D, Bozzette S: The ... 11 0 22 18 9 11 62 31 10 1 40 399 2304 61 21 19 Total 14 25 14 25 2850 Page of 14 (page number not for citation purposes) Retrovirology 2008, 5 :11 0 http://www.retrovirology.com/content/5 /1/ 110 Table...

Ngày tải lên: 13/08/2014, 05:21

Ngày tải lên: 30/06/2013, 01:26

... be cleaner A and B only C both D.not only 10 0.Lan dropped his watch when he was .the bus A.turning off B getting off C.taking off D.going off 10 1.Eater is a joyful festival which is celebrated ... true 10 2.The man is a manager is 45 years old A.Whom B.who C.what D.whose 10 3 my mum can sing very well, she has never sung a song in public A.But B.Despite C.Although D.Inspite of 10 4.My ... A.because B.but C.though D.so 10 5.I’ll bring a raincoat .it rains A.so B.in case C.but D.since 10 6 They sell jeans…………the world A.over all B all over C at over D over at 10 7.A new bridge is going...

Ngày tải lên: 28/08/2013, 15:10

... keep your answers to the point The interviewer doesn’t want to waste time and (16 ) you 10 11 12 13 14 15 16 A against A intend A his A anybody A number A colleagues A Attract A so B for B consider ... as what you (10 ) to say If you don’t own a video camera, perhaps a friend of (11 ) does Borrow it and make a video tape of yourself Find (12 ) to watch it with you and give you a (13 ) of advice ... (14 ) to dress At the interview, believe in yourself and be honest, open and friendly (15 ) attention and keep your answers to the point The interviewer doesn’t want to waste time and (16 ) you 10 ...

Ngày tải lên: 09/09/2013, 06:10