Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2eiaa1 -CCCCCCCCCCCCCHHHHHHHHHHHHHHCCCC-------HHHHHHHHHHHHHH------CCCCCCCCCCCCCCC----CC-CHHHHHHHCCCCC----------------- >P1;d3ds2a- -CCHHHCCCCCCCCHHHHHHHHHHHHHHCCCC-------HHHHHHHHHHHHHH------CCCHHHHHHHHHHCC----CC-CHHHHHHHHCCCCC------CCCCCCCC-- >P1;d3g21a- CCCHHHCCCCCCCCHHHHHHHHHHHHHCCCCC-------HHHHHHHHHHHHHH------HCCHHHHHHHCCCCC----CCCCHHHHHHHHHCCC----------------- >P1;d4bhxa1 ----------C--CHHHHHHHHHHC----CCCCCCCHHHHHHHHHHHHHHHHCHHHCCHHHHHHHHHHHHHHHHCC-------HHHHHHHHHHCCCCHHHHHHHHCCCCCC >P1;d4e6sa- ----------CCCCHHHHHHHHHCC----CCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCC-------HHHHHHHCCCCCCCHHHHHHCCC----- >P1;d4ph0a2 --CCCCCCCCCCCCHHHHHHHHHHHHHHHCCC-------CCCHHHHHHHHHHH------CCCHHHHHHHHH---HCCCCC-CHHHHHHHHCCCC----------------- >P1;d6saia1 -CCCCCCCCCCCCCHHHHHHHHHHHHHHCCCC-------HHHHHHHHHHHHHH------CCCCCCHHHHCCCCCCCCCCCCHHHHHHHHHHHCCC------CHHHHHHHHC PSA >P1;d2eiaa1 -a606626097915047008403630870a18-------a9437712220016------00297028306a173----73-738503620692f----------------- >P1;d3ds2a- -9407616068712071003404611692a27-------89517714751035------10087038306824a----c0-8685126308c202------82a6579b-- >P1;d3g21a- 47726706068a17046007503900562b26-------7a326620151067------2036a136207605b----9276183027104747----------------- >P1;d4bhxa1 ----------7--836531542472----8569a227771455467236501238627886266346127346606-------96025507858077184046117715a3 >P1;d4e6sa- ----------671849502651472----95598637a61654376035101348619992273147038526604-------88247509a2835547507641b----- >P1;d4ph0a2 --93571607991606600740571067405b-------d3548521372025------102950274059---6724a1-618603900392a----------------- >P1;d6saia1 -852132509b5370470054026306541b4-------76424620041024------100700210045319734ac5500530151063044------9606844a71 Translating the sequences -*C***CCCCCCCCHHHHHHHHHHHHH**CCC-------HHHHHHHHHHHHHH------*CC***********C----CC-*HHHHHHH**CCC----------------- -*C***CCCCCCCCHHHHHHHHHHHHH**CCC-------HHHHHHHHHHHHHH------*CCHHHHHHH****C----CC-*HHHHHHHH*CCC*------********-- **C***CCCCCCCCHHHHHHHHHHHHH**CCC-------HHHHHHHHHHHHHH------*CCHHHHHHH****C----CC**HHHHHHHH*CCC----------------- ----------C--CHHHHHHHHHH*----CCC*******HHHHHHHHHHHHH**********HHHHHHH*******-------HHHHHHH***C***************** ----------CCCCHHHHHHHHH**----CCC*******HHHHHHHHHHHHH**********HHHHHHH****C**-------HHHHHHH*CCC************----- --C***CCCCCCCCHHHHHHHHHHHHH**CCC-------***HHHHHHHHHHH------*CCHHHHHHH**---****CC-*HHHHHHHH*CCC----------------- -*C***CCCCCCCCHHHHHHHHHHHHH**CCC-------HHHHHHHHHHHHHH------*CC***HHHH****C****CC**HHHHHHHH**CC*------********** 47353.tem _________________________________ -*C***CCCCCCCCHHHHHHHHHHHHH**CCC-------HHHHHHHHHHHHHH------*CCHHHHHHH****C**--CC-*HHHHHHHH*CCC*------********-- Structural block scores 3 5 * 2.5 P 4.0 4.3 5.0 75.0 75.0 5.0 2.0 6 13 C 4.6 H 4.9 3.9 4.8 58.1 40.2 4.9 5.3 14 26 H 4.8 H 3.3 2.5 3.0 14.8 15.0 3.2 2.8 27 28 * 2.5 P 3.5 5.5 4.0 75.0 75.0 5.5 4.5 29 31 C 5.0 H 6.5 6.5 6.5 6.3 6.3 5.5 5.5 32 38 - 4.2 M 75.0 75.0 75.0 6.4 7.1 75.0 75.0 39 52 H 4.9 H 3.9 4.5 4.0 3.6 3.2 4.3 3.0 53 58 - 4.2 M 75.0 75.0 75.0 5.7 6.2 75.0 75.0 60 61 C 4.2 M 1.0 0.0 1.5 4.0 2.0 1.0 0.0 62 68 H 4.4 M 4.1 4.1 4.1 4.0 3.6 3.9 1.4 69 72 * 1.4 P 6.1 5.0 4.5 5.0 5.2 41.0 3.2 74 75 * 3.1 M 75.0 75.0 75.0 3.0 2.0 6.5 5.0 76 77 - 4.2 M 75.0 75.0 75.0 75.0 75.0 3.0 7.2 78 79 C 4.4 M 5.0 6.2 5.5 75.0 75.0 5.8 8.8 82 89 H 4.9 H 3.4 3.9 2.8 12.8 13.6 3.4 1.9 91 93 C 4.6 H 11.2 4.8 6.0 7.0 6.8 7.2 2.3 95 100 - 4.2 M 75.0 75.0 75.0 4.5 4.3 75.0 75.0 101 108 * 3.3 M 75.0 7.4 75.0 4.0 31.8 75.0 5.9 109 110 - 4.2 M 75.0 75.0 75.0 6.8 75.0 75.0 4.0 >>>>>>