This is multiRelief.py 1.0b Webserver at http://www.ibi.vu.nl/programs/shmrwww/ Please cite: Bernd Brandt*, K. Anton Feenstra* and Jaap Heringa "Multi-Harmony: detecting functional specificity from sequence alignment" Nucl. Acids Res., 2010, submitted * joint first authors. Calculating multi-Relief Found 33 sequences We now have 5 groups: group 1: 9 sequences label: 1(9) 1 1 gi|7160686|emb|CAB76819.1|/1-465 2 2 gi|61967924|gb|AAX56944.1|/1-465 3 3 gi|11464653|gb|AAG35265.1|/1-455 4 4 gi|6273783|gb|AAF06361.1|/1-472 5 5 gi|11907945|gb|AAG41407.1|/1-465 6 6 gi|29725652|gb|AAO88909.1|/1-465 7 7 gi|1654323|gb|AAC50790.1|/1-465 8 8 gi|3192871|gb|AAC19116.1|/1-468 9 9 gi|55926152|ref|NP_001007481.1|/1-464 group 2: 5 sequences label: 2(5) 10 1 gi|61967926|gb|AAX56945.1|/1-465 11 2 gi|2360958|gb|AAB92396.1|/1-465 12 3 gi|5706366|dbj|BAA83093.1|/1-465 13 4 gi|3982649|gb|AAC83580.1|/1-465 14 5 gi|6288777|gb|AAF06738.1|/1-464 group 3: 3 sequences label: 3(3) 15 1 gi|61967928|gb|AAX56946.1|/1-476 16 2 gi|2689629|gb|AAC53515.1|/1-434 17 3 gi|22532988|gb|AAF77079.2|/1-428 group 4: 8 sequences label: 4(8) 18 1 gi|2967646|gb|AAC39657.1|/1-467 19 2 gi|45331050|gb|AAS57861.1|/1-468 20 3 gi|5360217|dbj|BAA81909.1|/1-467 21 4 gi|6288775|gb|AAF06737.1|/1-468 22 5 gi|58047721|gb|AAH89184.1|/1-467 23 6 gi|4009524|gb|AAD11458.1|/1-486 24 7 gi|40254710|ref|NP_571441.2|/1-468 25 8 gi|18655485|pdb|1KHX|A|/22-226 group 5: 8 sequences label: 5(8) 26 1 gi|13992583|emb|CAC38118.1|/1-425 27 2 gi|11875329|dbj|BAB19634.1|/1-425 28 3 gi|45331052|gb|AAS57862.1|/1-422 29 4 gi|18418623|gb|AAL68976.1|/1-425 30 5 gi|2564493|gb|AAB81755.1|/1-425 31 6 gi|6981174|ref|NP_037227.1|/1-425 32 7 gi|45383213|ref|NP_989806.1|/1-426 33 8 gi|47523074|ref|NP_999302.1|/1-425 Calculating 528 pairwise distances Completed 0 out of 528 distance calculations (0%) Completed 6 out of 528 distance calculations (1%) Completed 15 out of 528 distance calculations (2%) Completed 21 out of 528 distance calculations (3%) Completed 28 out of 528 distance calculations (5%) Completed 36 out of 528 distance calculations (6%) Completed 45 out of 528 distance calculations (8%) Completed 55 out of 528 distance calculations (10%) Completed 66 out of 528 distance calculations (12%) Completed 78 out of 528 distance calculations (14%) Completed 91 out of 528 distance calculations (17%) Completed 105 out of 528 distance calculations (19%) Completed 120 out of 528 distance calculations (22%) Completed 136 out of 528 distance calculations (25%) Completed 153 out of 528 distance calculations (28%) Completed 171 out of 528 distance calculations (32%) Completed 190 out of 528 distance calculations (35%) Completed 210 out of 528 distance calculations (39%) Completed 231 out of 528 distance calculations (43%) Completed 253 out of 528 distance calculations (47%) Completed 276 out of 528 distance calculations (52%) Completed 300 out of 528 distance calculations (56%) Completed 325 out of 528 distance calculations (61%) Completed 351 out of 528 distance calculations (66%) Completed 378 out of 528 distance calculations (71%) Completed 406 out of 528 distance calculations (76%) Completed 435 out of 528 distance calculations (82%) Completed 465 out of 528 distance calculations (88%) Completed 496 out of 528 distance calculations (93%) Completed 528 out of 528 distance calculations (100%) Creating sequence indices Calculating relief weights comparing group 1; completed 1 out of 10 comparisons (10%) comparing group 2; completed 2 out of 10 comparisons (20%) comparing group 2; completed 3 out of 10 comparisons (30%) comparing group 3; completed 4 out of 10 comparisons (40%) comparing group 3; completed 5 out of 10 comparisons (50%) comparing group 3; completed 6 out of 10 comparisons (60%) comparing group 4; completed 7 out of 10 comparisons (70%) comparing group 4; completed 8 out of 10 comparisons (80%) comparing group 4; completed 9 out of 10 comparisons (90%) comparing group 4; completed 10 out of 10 comparisons (100%) Will do 100 randomizations of 5 groups [9, 5, 3, 8, 8]: calculated 0 out of 100 randomizations (0%) calculated 1 out of 100 randomizations (1%) calculated 2 out of 100 randomizations (2%) calculated 3 out of 100 randomizations (3%) calculated 4 out of 100 randomizations (4%) calculated 5 out of 100 randomizations (5%) calculated 6 out of 100 randomizations (6%) calculated 7 out of 100 randomizations (7%) calculated 8 out of 100 randomizations (8%) calculated 9 out of 100 randomizations (9%) calculated 10 out of 100 randomizations (10%) calculated 11 out of 100 randomizations (11%) calculated 12 out of 100 randomizations (12%) calculated 13 out of 100 randomizations (13%) calculated 14 out of 100 randomizations (14%) calculated 15 out of 100 randomizations (15%) calculated 16 out of 100 randomizations (16%) calculated 17 out of 100 randomizations (17%) calculated 18 out of 100 randomizations (18%) calculated 19 out of 100 randomizations (19%) calculated 20 out of 100 randomizations (20%) calculated 21 out of 100 randomizations (21%) calculated 22 out of 100 randomizations (22%) calculated 23 out of 100 randomizations (23%) calculated 24 out of 100 randomizations (24%) calculated 25 out of 100 randomizations (25%) calculated 26 out of 100 randomizations (26%) calculated 27 out of 100 randomizations (27%) calculated 28 out of 100 randomizations (28%) calculated 29 out of 100 randomizations (29%) calculated 30 out of 100 randomizations (30%) calculated 31 out of 100 randomizations (31%) calculated 32 out of 100 randomizations (32%) calculated 33 out of 100 randomizations (33%) calculated 34 out of 100 randomizations (34%) calculated 35 out of 100 randomizations (35%) calculated 36 out of 100 randomizations (36%) calculated 37 out of 100 randomizations (37%) calculated 38 out of 100 randomizations (38%) calculated 39 out of 100 randomizations (39%) calculated 40 out of 100 randomizations (40%) calculated 41 out of 100 randomizations (41%) calculated 42 out of 100 randomizations (42%) calculated 43 out of 100 randomizations (43%) calculated 44 out of 100 randomizations (44%) calculated 45 out of 100 randomizations (45%) calculated 46 out of 100 randomizations (46%) calculated 47 out of 100 randomizations (47%) calculated 48 out of 100 randomizations (48%) calculated 49 out of 100 randomizations (49%) calculated 50 out of 100 randomizations (50%) calculated 51 out of 100 randomizations (51%) calculated 52 out of 100 randomizations (52%) calculated 53 out of 100 randomizations (53%) calculated 54 out of 100 randomizations (54%) calculated 55 out of 100 randomizations (55%) calculated 56 out of 100 randomizations (56%) calculated 57 out of 100 randomizations (57%) calculated 58 out of 100 randomizations (58%) calculated 59 out of 100 randomizations (59%) calculated 60 out of 100 randomizations (60%) calculated 61 out of 100 randomizations (61%) calculated 62 out of 100 randomizations (62%) calculated 63 out of 100 randomizations (63%) calculated 64 out of 100 randomizations (64%) calculated 65 out of 100 randomizations (65%) calculated 66 out of 100 randomizations (66%) calculated 67 out of 100 randomizations (67%) calculated 68 out of 100 randomizations (68%) calculated 69 out of 100 randomizations (69%) calculated 70 out of 100 randomizations (70%) calculated 71 out of 100 randomizations (71%) calculated 72 out of 100 randomizations (72%) calculated 73 out of 100 randomizations (73%) calculated 74 out of 100 randomizations (74%) calculated 75 out of 100 randomizations (75%) calculated 76 out of 100 randomizations (76%) calculated 77 out of 100 randomizations (77%) calculated 78 out of 100 randomizations (78%) calculated 79 out of 100 randomizations (79%) calculated 80 out of 100 randomizations (80%) calculated 81 out of 100 randomizations (81%) calculated 82 out of 100 randomizations (82%) calculated 83 out of 100 randomizations (83%) calculated 84 out of 100 randomizations (84%) calculated 85 out of 100 randomizations (85%) calculated 86 out of 100 randomizations (86%) calculated 87 out of 100 randomizations (87%) calculated 88 out of 100 randomizations (88%) calculated 89 out of 100 randomizations (89%) calculated 90 out of 100 randomizations (90%) calculated 91 out of 100 randomizations (91%) calculated 92 out of 100 randomizations (92%) calculated 93 out of 100 randomizations (93%) calculated 94 out of 100 randomizations (94%) calculated 95 out of 100 randomizations (95%) calculated 96 out of 100 randomizations (96%) calculated 97 out of 100 randomizations (97%) calculated 98 out of 100 randomizations (98%) calculated 99 out of 100 randomizations (99%) Output multi-Relief weights Alignment Position multi-Relief Weights Support Positive Support Negative Z_scores 1(9) Consensus string 2(5) Consensus string 3(3) Consensus string 4(8) Consensus string 5(8) Consensus string 1 0.196006944444 0.5 0.0 1.60335103082 Dt D ND D D 2 0.955729166667 0.8 0.0 5.321183078 Vm V F La L 3 0.578373015873 0.7 0.0 4.00831142293 Qh Q R Qa Q 4 0.831380208333 0.4 0.0 6.42856975653 Ap P P P P 5 0.0 0.0 0.0 nan V V V V V 6 0.918229166667 0.8 0.0 5.13131688664 An Ae C Tm T 7 0.0 0.0 0.0 nan Y Y Y Y Y 8 0.727777777778 0.9 0.0 4.78121210648 Eq Eq E Sh C 9 0.0 0.0 0.0 nan E E E E E 10 0.0 0.0 0.0 -0.442371750026 P P P P Ps 11 0.795833333333 0.8 0.0 4.66355249131 K Ks LQ A A 12 0.981481481481 0.6 0.0 5.17272247605 Hy H H F F 13 0.0 0.0 0.0 nan W W W W W 14 0.0 0.0 0.0 nan C C C C C 15 0.0 0.0 0.0 nan S S S S S 16 1.0 0.4 0.0 6.49173552729 I I V I I 17 0.96875 0.8 0.0 6.24239371071 V V A As S 18 0.0 0.0 0.0 nan Y Y Y Y Y 19 0.0 0.0 0.0 nan Y Y Y Y Y 20 0.0 0.0 0.0 nan E E E E E 21 0.0 0.0 0.0 nan L L L L L 22 0.0 0.0 0.0 nan N N N N N 23 0.96875 0.6 0.0 5.48636570174 N N N Qt Q 24 0.0 0.0 0.0 nan R R R R R 25 0.0 0.0 0.0 nan V V V V V 26 0.0 0.0 0.0 nan G G G G G 27 0.0 0.0 0.0 nan E E E E E 28 1.0 0.6 0.0 5.39611682116 A A T T T 29 0.0 0.0 0.0 0.0923250999054 F Fy F F F 30 0.779340277778 0.5 0.0 5.04792508323 Hln H Q H H 31 0.0 0.0 0.0 nan A A A A A 32 0.0 0.0 0.0 nan S S S S S 33 0.96166087963 0.6 0.0 4.99689296357 Sq S S Q Q 34 0.979166666667 0.8 0.0 5.41213644519 Tl T R P P 35 0.0 0.0 0.0 nan S S S S S 36 0.701786747685 0.8 0.2 4.98046380675 IV V IV Li Ml 37 0.981481481481 0.6 0.0 5.17272247605 Li L L T T 38 0.779340277778 0.5 0.0 4.70415294926 Vi V I V V 39 0.0 0.0 0.0 nan D D D D D 40 0.0 0.0 0.0 nan G G G G G 41 0.0 0.0 0.0 nan F F F F F 42 0.0 0.0 0.0 nan T T T T T 43 0.0 0.0 0.0 nan D D D D D 44 0.0 0.0 0.0 nan P P P P P 45 -0.2 0.0 0.4 -2.66225470453 S Sa S S S 46 0.0 0.0 0.0 nan N N N N N 47 0.96875 0.6 0.0 5.26710356226 N N N S Sa 48 0.707638888889 0.8 0.1 4.75046437629 Ksr K KR - - 49 0.761111111111 0.8 0.0 5.16471501112 Nd NS N E E 50 0.0 0.0 0.0 nan R R R R R 51 -0.15625 0.0 0.4 -1.98454411199 F F F F Fl 52 0.0 0.0 0.0 nan C C C C C 53 0.0 0.0 0.0 nan L L L L L 54 -0.15625 0.0 0.4 -2.20194508658 G G G Gc G 55 0.0 0.0 0.0 nan L L L L L 56 0.0 0.0 0.0 nan L L L L L 57 0.0 0.0 0.0 nan S S S S S 58 0.0 0.0 0.0 nan N N N N N 59 0.0 0.0 0.0 nan V V V V V 60 0.0 0.0 0.0 nan N N N N N 61 0.0 0.0 0.0 nan R R R R R 62 0.0 0.0 0.0 nan N N N N N 63 0.96875 0.6 0.0 5.48636570174 S S S Ae A 64 0.798611111111 0.5 0.0 6.1571468015 T T T Tv A 65 1.0 0.6 0.0 5.3782049024 I I I V V 66 0.0 0.0 0.0 nan E E E E E 67 0.964285714286 0.7 0.0 7.18980909756 N N N Mq L 68 0.0 0.0 0.0 nan T T T T T 69 0.0 0.0 0.0 nan R R R R R 70 0.0 0.0 0.0 nan R R R R R 71 0.0 0.0 0.0 nan H H H H H 72 0.0 0.0 0.0 nan I I I I I 73 0.0 0.0 0.0 nan G G G G G 74 0.928240740741 0.6 0.0 5.08062295994 K K K Rk R 75 0.0 0.0 0.0 nan G G G G G 76 0.0 0.0 0.0 nan V V V V V 77 1.0 0.6 0.0 5.3782049024 H H H R R 78 0.0 0.0 0.0 nan L L L L L 79 0.0 0.0 0.0 nan Y Y Y Y Y 80 0.0 0.0 0.0 nan Y Y Y Y Y 81 1.0 0.6 0.0 5.3782049024 V V V I I 82 0.0 0.0 0.0 nan G G G G G 83 0.0 0.0 0.0 nan G G G G G 84 0.0 0.0 0.0 nan E E E E E 85 0.0 0.0 0.0 nan V V V V V 86 1.0 0.6 0.0 5.3782049024 Y Y Y F F 87 0.0 0.0 0.0 nan A A A A A 88 0.0 0.0 0.0 nan E E E E E 89 0.0 0.0 0.0 nan C C C C C 90 1.0 0.4 0.0 6.49173552729 L L V L L 91 0.0 0.0 0.0 nan S S S S S 92 0.0 0.0 0.0 nan D D D D D 93 -0.15625 0.0 0.4 -2.12225528499 S St S S Sn 94 0.928240740741 0.6 0.0 5.08062295994 S S S As A 95 0.0 0.0 0.0 nan I I I I I 96 0.0 0.0 0.0 nan F F F F F 97 0.0 0.0 0.0 nan V V V V V 98 0.0 0.0 0.0 nan Q Q Q Q Q 99 0.0 0.0 0.0 nan S S S S S 100 1.0 0.6 0.0 5.3782049024 R R R P P 101 0.0 0.0 0.0 nan N N N N N 102 0.0 0.0 0.0 nan C C C C C 103 0.0 0.0 0.0 nan N N N N N 104 0.721666666667 0.8 0.1 5.02978035102 Yf YF Y Q Q 105 1.0 0.8 0.0 5.57333037497 H H Q R R 106 1.0 0.6 0.0 5.3782049024 H H H Y Y 107 -0.154296875 0.0 0.4 -2.29580883554 Gn G G Gd G 108 1.0 0.6 0.0 5.3782049024 F F F W W 109 0.0 0.0 0.0 nan H H H H H 110 0.0 0.0 0.0 nan P P P P P 111 1.0 0.6 0.0 5.39611682116 T T A A A 112 0.0 0.0 0.0 nan T T T T T 113 0.0 0.0 0.0 nan V V V V V 114 0.0 0.0 0.0 nan C C C C C 115 0.0 0.0 0.0 nan K K K K K 116 0.0 0.0 0.0 nan I I I I I 117 0.0 0.0 0.0 nan P P P P P 118 0.96166087963 0.6 0.0 4.99689296357 Sp S S P P 119 0.186111111111 0.4 0.3 0.954439973463 Gr GS G G G 120 0.0 0.0 0.0 nan C C C C C 121 1.0 0.6 0.0 5.3782049024 S S S N N 122 0.0 0.0 0.0 nan L L L L L 123 0.0 0.0 0.0 nan K K K K K 124 0.416666666667 0.4 0.0 3.57537631008 I I IV I I 125 0.0 0.0 0.0 nan F F F F F 126 0.0078125 0.1 0.0 0.153334436735 Ns N N N N 127 0.0 0.0 0.0 nan N N N N N 128 0.0 0.0 0.0 nan Q Q Q Q Q 129 1.0 0.4 0.0 6.49173552729 E E L E E 130 0.0 0.0 0.0 nan F F F F F 131 -0.166666666667 0.0 0.4 -1.96553592121 - - A- - - 132 -0.166666666667 0.0 0.4 -1.96553592121 - - Q- - - 133 -0.166666666667 0.0 0.4 -1.96553592121 - - L- - - 134 -0.166666666667 0.0 0.4 -1.96553592121 - - L- - - 135 0.0 0.0 0.0 nan A A A A A 136 0.962962962963 0.6 0.0 4.93377662373 Qeh Q Q A A 137 0.25 0.4 0.0 2.40241090044 L L PL L L 138 0.0 0.0 0.0 nan L L L L L 139 -0.0633680555556 0.0 0.1 -0.907431536569 As A A As A 140 0.0078125 0.1 0.0 0.153334436735 Qr Q Q Q Q 141 0.0078125 0.1 0.0 0.153334436735 St S S S S 142 0.0 0.0 0.0 nan V V V V V 143 0.394965277778 0.4 0.0 2.91779812127 Nh N NH Ns N 144 1.0 0.6 0.0 5.3782049024 H H H Q Q 145 0.0 0.0 0.0 nan G G G G G 146 0.0 0.0 0.0 nan F F F F F 147 0.0 0.0 0.0 nan E E E E E 148 0.919518849206 0.7 0.0 6.36487899413 Ta A V A A 149 0.0 0.0 0.0 nan V V V V V 150 0.0 0.0 0.0 nan Y Y Y Y Y 151 0.96875 0.6 0.0 5.26710356226 E E E Q Qr 152 0.0 0.0 0.0 nan L L L L L 153 0.0 0.0 0.0 nan T T T T T 154 1.0 0.6 0.0 5.3782049024 K K K R R 155 0.0 0.0 0.0 nan M M M M M 156 0.0 0.0 0.0 nan C C C C C 157 0.0 0.0 0.0 nan T T T T T 158 -0.130353009259 0.0 0.4 -2.75856634956 Il I I I I 159 0.0 0.0 0.0 nan R R R R R 160 0.0 0.0 0.0 nan M M M M M 161 0.0 0.0 0.0 nan S S S S S 162 0.0 0.0 0.0 nan F F F F F 163 0.0 0.0 0.0 nan V V V V V 164 0.0 0.0 0.0 nan K K K K K 165 0.0 0.0 0.0 nan G G G G G 166 0.0 0.0 0.0 nan W W W W W 167 0.0 0.0 0.0 nan G G G G G 168 0.0 0.0 0.0 nan A A A A A 169 -0.0555555555556 0.0 0.4 -0.930362957483 Ek E E E E 170 0.0 0.0 0.0 nan Y Y Y Y Y 171 1.0 0.6 0.0 5.3782049024 H H H R R 172 0.0 0.0 0.0 nan R R R R R 173 0.0 0.0 0.0 nan Q Q Q Q Q 174 1.0 0.6 0.0 5.3782049024 D D D T T 175 0.0 0.0 0.0 nan V V V V V 176 0.0 0.0 0.0 nan T T T T T 177 0.0 0.0 0.0 nan S S S S S 178 0.0 0.0 0.0 nan T T T T T 179 0.0 0.0 0.0 nan P P P P P 180 0.0 0.0 0.0 nan C C C C C 181 0.0 0.0 0.0 nan W W W W W 182 0.0078125 0.1 0.0 0.153334436735 Iv I I I I 183 0.0 0.0 0.0 nan E E E E E 184 0.966666666667 0.6 0.0 5.11537019291 I Iv I L L 185 0.0 0.0 0.0 nan H H H H H 186 0.0 0.0 0.0 nan L L L L L 187 0.96166087963 0.6 0.0 4.99689296357 Hn H H N N 188 0.0 0.0 0.0 nan G G G G G 189 0.0 0.0 0.0 nan P P P P P 190 0.0 0.0 0.0 nan L L L L L 191 0.0 0.0 0.0 nan Q Q Q Q Q 192 0.0 0.0 0.0 nan W W W W W 193 0.0 0.0 0.0 nan L L L L L 194 0.0 0.0 0.0 nan D D D D D 195 -0.0633680555556 0.0 0.1 -0.907431536569 Kr K K Kr K 196 0.0 0.0 0.0 nan V V V V V 197 0.0 0.0 0.0 nan L L L L L 198 0.0 0.0 0.0 nan T T T T T 199 0.0 0.0 0.0 nan Q Q Q Q Q 200 0.0 0.0 0.0 nan M M M M M 201 0.0 0.0 0.0 nan G G G G G 202 0.0078125 0.1 0.0 0.153334436735 St S S S S 203 0.0 0.0 0.0 nan P P P P P 204 0.924370659722 0.8 0.0 6.75453067734 Hr L H Sr Sn 205 0.928571428571 0.7 0.0 7.55651209219 N N N Vl Il 206 0.928240740741 0.6 0.0 5.08062295994 P P P Rp R 207 1.0 0.6 0.0 5.3782049024 I I I C C 208 0.0 0.0 0.0 nan S S S S S 209 0.0 0.0 0.0 nan S S S S S 210 1.0 0.4 0.0 8.72993036775 V V V M V 211 0.0 0.0 0.0 nan S S S S S