Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1qgoa- ---CEEEEEEECCCCC----------------------------------------------------HHHHHHHHHHHHHHHHHCCC-CCEEEEEECCHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCEEEEEECCCCCCHH-HHHHHHHHHHHHH-H---CC-EEEECCCCCCCHHHHHHHHHHHHCCCC-CCC----CCEEEEEEECCCC-------HHHHHHHHHHHHHHHHH---CCCEEEEECC--------CCCC-HHHHHHHHHHHCCCEEEEEEC-CCCCCHHHHCCCCCCCCCCHHHHHHH-CC-------------CCEEECCCCHHHCHHHHHHHHHHHHHHHHC-------------------------------- >P1;d2h1va- CCEEEEEEEEECCCCCCHHHHHHHHHHHCC-------------CCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCC-EEEEEEEEECCCC-----------CCHHHHHHHHHHCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHC---CCEEEECCCCCCCHHHHHHHHHHHHHHH-HHCCHHHHCCEEEEEEEECCCHHHHHHCCCHHHHHHHHHHHHHHHHCCC-CEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHCCCCC----HHHHHHHH-HC-------------C-EEECCCCCCCCHHHHHHHHHHHHHHCCC-------------------------------- >P1;d2xvxa- --CCEEEEEEECCCCC----------------------------------------------------CCCCHH-HHHHHHHHHHHCC-CCCEEEEECCHHHHHHHHHC-CCCCCCHHHHHHHHHHCCCCEEEEEECCCCCCHH-HHHHHHHHHHHCC-CCCCCC-EEEEECCCCCCHHHHHHHHHHHHHHCCCCCC----CCCCEEEEECCCC-------CHHHHHHHHHHHHHHHH---CCCEEEEECC--------CCCC-HHHHHHHHHHHCCCEEEEEEC-CCCCCHHHHCCCCCCCCCCHHHHHHH-CC-------------CEEEECCCCHHHCHHHHHHHHHHHHHHHHCCC------------------------------ >P1;d2xwsa1 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCEEEEEEECCCCC------HHHHHHHHHHHHHHHHH-CCCCEEEEEECCC------CCCCCHHHHHHHC----CCCEEEEEEC-CCCCC------------HHHHCHHHHHHCCCCCCCCEEEEECCEEEEECCCCCCCHHHHHHHHHHHHCC----------------------------------C >P1;d3hcna- CCCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCHHHCCEEEEEEECCCC-----------CCHHHHHHHHHHCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHH-CCCCCCCHHHCEEEEEEECCCHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEEECC-CCCCCCCCCCHHHHHHHHHHC-CCCEEEEECCCCCCCCCCCHHHHCH----HHHHHHHHHCC-------------CCEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHCCCCCCCCCHHHHHHHHHHCCCC PSA >P1;d1qgoa- ---6400000050015----------------------------------------------------59107500320083027307-8063320011671174068429460240360055028590710000001013075-0550361077147-5---08-401004000177901550070056202-b07----8522000005464-------73046003401810666---9120100008--------1515-07700730585a062020000-11103630364003889800123049-1a-------------060525440002063027003500360198-------------------------------- >P1;d2h1va- c35500000013100256820470224348-------------8770778516712540860a60860062045007303730273295-0404000000106-----------3103500450383a074000000300102620540162054108737---c090500620160740150014105711-770497138400000003001460597a030091064006300770a0a-4220000247b7986103410371047138656030000000010022120211026----20450066-09-------------0-41201700214940030002001631a6-------------------------------- >P1;d2xvxa- --64200000040015----------------------------------------------------790350-1850081058516-a2403101018911550585-a3a0321561069029590320000001012184-0590393047238-68a206-300004000078910430060046202b916----9710000003019-------28128203800610453---2720000015--------2715-086007305829183000100-00003720264002b69900122076-4a-------------0603313600042850050025006601740c------------------------------ >P1;d2xwsa1 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------65300000031468------97236305541463566-8624302200006------9273202300770----a061030302-17818------------73013400520a075776616671582401035040a6a9267784588589----------------------------------b >P1;d3hcna- 872300000003000673a5026002311306023927808830362078316613531531a3003038303500560184038406a01104200001016-----------3104400450272607300000000000113010000002410784a7916030100000121700030005005500-65057854870000000500238128250201900530054004509540527100013-549472246300820442047-7340000000010051230401137----85456048616-------------14414105001428201600031027006585203960484077193812750251037186 Translating the sequences ---CEEEEEEECCCCC----------------------------------------------------HHHHHHHHHHHHHHHHH*CC-*C*EEEEE*****************CCHHHHHHHHHHCCCCEEEEEECCCCCC**-HHHHHHHHHHHHH-*---CC-EEEE*CCCCCCHHHHHHHHHHHH****-CCC----CCEEEEEEECCCC-------*HHHHHHHHHHHHHHHH---CCCEEEEECC--------CCCC-HHHHHHHHHHHCCCEEEEEEC-CCCCCHHHHCCCCC*****HHHHHHH-CC-------------C*EEECCCC***CHHHHHHHHHHHHHHHHC-------------------------------- ****EEEEEEECCCCC**************-------------*************************HHHHHHHHHHHHHHHHHHCC*-**EEEEE******-----------CCHHHHHHHHHHCCCCEEEEEECCCCCC***HHHHHHHHHHHHH**C---C*EEEE*CCCCCCHHHHHHHHHHHHHH*-**CC****CCEEEEEEE*CCC*******C*HHHHHHHHHHHHHHH*CCC-CEEEEE*CC******CCCCCHHHHHHHHHHHHCCCEEEEE*C*CCCCCHHHHCCCCC----HHHHHHHH-*C-------------C-EEECCCCCCCCHHHHHHHHHHHHHH**C-------------------------------- --*CEEEEEEECCCCC----------------------------------------------------****HH-HHHHHHHHHHHCC-*C*EEEEE************-****CCHHHHHHHHHHCCCCEEEEEECCCCCC**-HHHHHHHHHHH**-*C**CC-EEEE*CCCCCCHHHHHHHHHHHHHH***CCC----CC**EEEEECCCC-------CHHHHHHHHHHHHHHHH---CCCEEEEECC--------CCCC-HHHHHHHHHHHCCCEEEEEEC-CCCCCHHHHCCCCC*****HHHHHHH-CC-------------C*EEECCCC***CHHHHHHHHHHHHHHHHC**------------------------------ ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCEEEEEEECCCC*------*HHHHHHHHHHHHHHHH-CCCC*EEEEECCC------CCCCCHHHHHHH*----CCCEEEEEEC-CCCCC------------*HHH*HHHH**C*************C*EEE*CCCCCCCHHHHHHHHHHHH**----------------------------------* ***CEEEEEEECCCCC****************************************************HHHHHHHHHHHHHHHHHHC***C*EEEEE******-----------CCHHHHHHHHHHCCCCEEEEEECCCCCC***HHHHHHHHHHHHH**C**CC*EEEE*CCCCCCHHHHHHHHHHHHHH*-*CCC*******EEEEEE*CCC*******C*HHHHHHHHHHHHHHH*CCCCCEEEEE*CC-*****CCCCCHHHHHHHHHH*-CCCEEEEE*C*CCCCC***H***C*----HHHHHHHH*CC-------------C*EEE*CCCCCCCHHHHHHHHHHHHHHHH********************************* 53800.tem _________________________________ --*CEEEEEEECCCCC----------------------------------------------------HHHHHHHHHHHHHHHHHHCC-*C*EEEEE******-----------CCHHHHHHHHHHCCCCEEEEEECCCCCC**-HHHHHHHHHHHHH-*C--CC-EEEE*CCCCCCHHHHHHHHHHHHHH*-*CCC----CCEEEEEEECCCC*------CHHHHHHHHHHHHHHHH-CCCCCEEEEECCC------CCCCCHHHHHHHHHHHHCCCEEEEEEC-CCCCCHHHHCCCCC---*HHHHHHHH-CC-------------C*EEECCCCCCCCHHHHHHHHHHHHHHHHC-------------------------------- Structural block scores 0 1 - 3.8 M 75.0 7.8 75.0 75.0 7.5 4 10 E 4.5 M 0.6 0.1 0.3 75.0 0.0 11 15 C 4.5 M 2.2 1.2 2.0 75.0 1.8 16 67 - 4.0 M 75.0 22.1 75.0 75.0 3.5 68 85 H 4.4 M 3.1 2.9 7.8 75.0 3.4 86 87 C 4.3 M 3.5 5.5 3.5 75.0 3.0 92 96 E 4.5 M 1.6 0.8 1.0 75.0 1.2 97 102 * 2.1 P 2.8 1.2 3.3 75.0 1.3 103 113 - 3.9 M 4.5 75.0 11.5 75.0 75.0 114 115 C 4.5 M 3.0 2.0 2.5 75.0 2.0 116 125 H 4.5 M 2.9 2.8 3.9 75.0 2.6 126 129 C 4.5 M 5.2 5.1 4.2 75.0 3.8 130 135 E 4.5 M 0.2 0.7 0.3 75.0 0.5 136 141 C 4.5 M 0.8 0.7 0.8 75.0 0.0 142 143 * 2.1 P 6.0 4.0 6.0 75.0 1.0 145 157 H 4.4 M 3.5 2.8 4.1 75.0 1.2 161 162 - 3.8 M 75.0 75.0 6.2 75.0 8.0 163 164 C 4.3 M 4.0 43.8 3.0 75.0 3.5 166 169 E 4.5 M 1.2 3.5 0.8 75.0 1.0 171 176 C 4.5 M 2.0 2.5 1.8 75.0 0.7 177 190 H 4.4 M 3.4 2.6 3.1 75.0 1.8 194 196 C 4.4 M 6.2 3.7 5.3 75.0 3.3 197 200 - 3.8 M 75.0 5.0 75.0 75.0 6.0 201 202 C 4.5 M 6.5 6.0 8.0 5.5 7.5 203 209 E 4.8 H 0.6 0.0 0.1 0.4 0.0 210 213 C 4.7 H 4.8 1.0 3.2 3.5 1.8 215 220 - 3.8 M 75.0 6.2 75.0 75.0 4.3 222 237 H 4.9 H 3.0 2.9 3.2 4.1 2.4 239 243 C 4.5 M 32.4 20.0 32.2 4.6 4.6 244 248 E 5.0 H 0.2 0.8 0.0 0.8 2.0 249 251 C 4.3 M 27.7 2.0 27.0 2.0 1.3 252 257 - 3.9 M 75.0 8.1 75.0 75.0 17.3 258 262 C 4.8 H 17.4 1.8 18.0 4.6 3.4 263 274 H 4.7 H 9.8 3.8 9.5 26.6 8.8 275 277 C 5.0 H 5.5 3.0 6.0 5.5 4.7 278 283 E 4.8 H 0.7 0.0 0.7 1.2 0.0 286 290 C 5.0 H 1.2 1.0 0.6 5.0 1.4 291 294 H 4.2 M 3.0 1.2 2.8 75.0 2.2 295 299 C 4.2 M 2.6 2.0 2.4 75.0 2.4 300 302 - 3.8 M 8.3 75.0 8.8 75.0 75.0 304 311 H 4.8 H 2.4 2.9 2.2 2.0 5.0 313 314 C 4.4 M 5.8 4.5 7.2 5.2 3.5 315 327 - 4.5 M 75.0 75.0 75.0 4.9 75.0 330 332 E 5.0 H 2.3 2.3 2.0 1.7 3.0 333 340 C 4.4 M 1.9 1.9 2.0 3.6 1.6 341 356 H 4.8 H 2.8 2.5 2.8 15.4 2.2 358 389 - 4.4 M 75.0 75.0 70.7 73.0 4.1 >>>>>>