Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1e0ta1 ------------------------------------------CCEECCCCHHH--CCEEE-CCCEEEEECCCCC--------------CCCC-CEEECCCCCHHHHCCCCCEEEECCCCEEEEEEEE-EC-----------------------------CEEEEEECCCEEECCCCEEECCCCCCCC------------------------------------------------------ >P1;d1o65a1 CHHHHHCCEECCEEEECCCEEECC--EEEEECCEECCCCCC-----------------CCHHHHCEEEEECHHHHHHHHHCHHHHHHCCCCCCCCCEEECCCCCCCCCCCCEEEECC--EEEEEEEECCCCCHHHHHC-----CCCCHHHHHHHH--CCCCEEEEEEECEEEECCCCEEEEECCCCCCHHHHHHHHHCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHC >P1;d1orua- ---CCCCEEEEEECCCCCCCCCCCCCEEEECCCCCCCCCCCCCEEECCCCCCCCCCCEEECC-CCEEEEEHHHHHHHHHC---CCCCCCHHHHCCCEEEECCCHHHCCCCCEEECCCC-CEEEEEEECCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCEEEEEEECEEEECCCEEEEECCC--------------------------------------------------------- >P1;d2g50a1 ------------------------------------------CCEECCCCCCCCCCCEEECCCCEEEEECCHHHCC------------CCCC-CEEECCCCCHHHHCCCCCEEEECCCCEEEEEEEE-EC-----------------------------CEEEEEEEECEEECCCCEEECCCCCCCC------------------------------------------------------ >P1;d3hqna2 -------------------------------------------CCCCCCCHH---HCCEECCCCEEEEECCHHHCC------------CCCC-CEEECCCCCHHHHCCCCCEEEECCCCEEEEEEEEEEC-----------------------------CEEEEEECCCEECCCCCCEECCCCCCCC------------------------------------------------------ PSA >P1;d1e0ta1 ------------------------------------------970301706a5--86170-5646010024592--------------5034-8300041840181076734020395501040531-8c-----------------------------4403050358360128340704c1a273------------------------------------------------------ >P1;d1o65a1 79439684518040104918429a--51404661059185b-----------------b3452500100034008203742692484070110700000780305502000205057--0401001013043610750-----909400330063--120001020444250119330205314180106400300042834493063016053009705730460276682582683042 >P1;d1orua- ---4764140300020459733065a4060571003b0353483380482276976571505-20010004400650084---b0660302001000002967106166503030534-01020105070456005203751693891274048306610000020472520544170422155--------------------------------------------------------- >P1;d2g50a1 ------------------------------------------870400403c9a9950407865803000668446------------7015-8100040640071086633030294700030483-18-----------------------------6303040471660135350705c0a253------------------------------------------------------ >P1;d3hqna2 -------------------------------------------80401307c---750606795403000367347------------5056-730104064018107461503018160302045456a-----------------------------500303034534053644070480b365------------------------------------------------------ Translating the sequences ------------------------------------------CCEECCCC***--CCEEE-CCCEEEEECC***--------------CCCC-CEEECCCCCHHHHCCCCCEEEECCCCEEEEEEEE-EC-----------------------------CEEEEEE**CEEECCCCEEECCCCCCCC------------------------------------------------------ ************************--***************-----------------*******EEEE*CHHH**************CCCC*C**E**CCC****CCCCCEEEECC--EEEEEEEE**C********-----************--**C*EEEEEEECEEE*CCC*EE***CCCCC****************************************************** ---***************************************C*EECCCC*****CCEEECC-C*EEEE**HHH******---*****C****C**E***CC*HHHCCCCCEEE*CCC-*EEEEEEE**C*****************************C*EEEEEEECEEE*CCCEEE**CCC--------------------------------------------------------- ------------------------------------------CCEECCCC*****CCEEECCCCEEEEECCHHH**------------CCCC-CEEECCCCCHHHHCCCCCEEEECCCCEEEEEEEE-EC-----------------------------CEEEEEEEECEEECCCCEEECCCCCCCC------------------------------------------------------ -------------------------------------------C**CCCC**---*C*EECCCCEEEEECCHHH**------------CCCC-CEEECCCCCHHHHCCCCCEEEECCCCEEEEEEEE*EC-----------------------------CEEEEEE**CEE*CCCC*EECCCCCCCC------------------------------------------------------ 50800.tem _________________________________ ------------------------------------------CCEECCCC***--CCEEECCCCEEEEECCHHH**------------CCCC-CEEECCCCCHHHHCCCCCEEEECCCCEEEEEEEE*EC-----------------------------CEEEEEEEECEEECCCCEEECCCCCCCC------------------------------------------------------ Structural block scores 0 41 - 3.9 M 75.0 9.7 8.6 75.0 75.0 42 43 C 4.2 M 8.0 75.0 5.5 7.5 41.5 44 45 E 4.1 M 1.5 75.0 5.5 2.0 2.0 46 49 C 4.5 M 2.0 75.0 3.5 1.0 1.0 50 52 * 2.4 P 7.2 75.0 5.0 8.2 31.5 53 54 - 3.8 M 75.0 75.0 8.0 9.8 75.0 55 56 C 4.3 M 7.0 75.0 5.5 7.0 6.0 57 59 E 4.4 M 2.7 29.8 4.3 1.3 2.0 60 63 C 4.3 M 22.5 4.0 20.5 6.5 6.8 64 68 E 4.8 H 1.4 0.2 0.2 2.2 1.4 69 70 C 4.2 M 3.0 1.5 2.0 3.0 1.5 71 73 H 4.5 M 5.3 1.3 1.3 6.0 5.3 74 75 * 2.1 P 75.0 5.0 5.5 5.0 5.5 76 87 - 4.0 M 75.0 4.1 21.7 75.0 75.0 88 91 C 4.6 H 3.0 2.2 1.2 3.2 4.0 94 96 E 4.2 M 1.0 0.0 0.0 0.3 1.3 97 101 C 4.4 M 3.4 3.0 3.4 2.8 2.8 102 105 H 4.3 M 2.5 3.2 3.5 2.0 2.5 106 110 C 5.0 H 4.6 0.4 3.6 4.6 3.6 111 114 E 4.9 H 1.5 1.8 1.5 1.5 2.0 115 118 C 4.7 H 5.5 40.5 21.8 5.5 4.0 119 126 E 4.9 H 1.8 0.8 1.1 2.2 2.2 130 158 - 4.0 M 75.0 20.4 4.0 75.0 75.0 160 167 E 4.5 M 2.5 1.4 1.6 2.6 1.6 169 171 E 4.8 H 3.0 2.3 2.3 4.0 2.3 172 175 C 4.7 H 3.5 3.5 3.5 3.0 4.5 176 178 E 4.6 H 3.7 1.7 3.7 4.0 3.7 179 186 C 4.5 M 5.0 2.8 30.0 4.8 4.7 187 240 - 4.5 M 75.0 3.4 75.0 75.0 75.0 >>>>>>