December 29 2007 9:08:40.348 AM SS_QG_ALIGN_PRB FORTRAN90 version Test SS_QG_ALIGN Sequence/sequence Quasiglobal Gap alignment. TEST01: SS_QG_FSQ - Forward score quadratic; SS_QG_FSL - Forward score linear; GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Verify that the FSQ and FSL tables agree. Sequences A and B: 1 G T 2 C A 3 T G 4 A 5 G 6 T 7 A 8 T 9 A 10 G 11 C 12 T Matching Scores: 0 0.0 0.0 0.0 0.0 1 0.0 -1.0 1.0 5.0 2 0.0 -3.0 -3.0 -5.0 3 0.0 4.0 1.0 -1.0 4 0.0 1.0 3.0 1.0 5 0.0 -1.0 1.0 5.0 6 0.0 4.0 1.0 -1.0 7 0.0 1.0 3.0 1.0 8 0.0 4.0 1.0 -1.0 9 0.0 1.0 3.0 1.0 10 0.0 -1.0 1.0 5.0 11 0.0 -3.0 -3.0 -5.0 12 0.0 4.0 1.0 -1.0 SS_QG_FSQ: 0 1 2 3 SF: 0 0.0 0.0 0.0 0.0 1 0.0 -1.0 1.0 5.0 2 0.0 -2.5 -1.5 2.5 3 0.0 4.0 1.5 2.0 4 0.0 1.5 7.0 4.5 5 0.0 1.0 4.5 12.0 6 0.0 4.0 4.0 9.5 7 0.0 1.5 7.0 9.0 8 0.0 4.0 4.5 8.5 9 0.0 1.5 7.0 8.0 10 0.0 1.0 4.5 12.0 11 0.0 0.5 4.0 9.5 12 0.0 4.0 3.5 9.0 EF: 0 0.0 0.0 0.0 0.0 1 -2.0 -2.5 -3.0 -1.5 2 -2.0 -2.5 -3.0 -3.5 3 -2.0 -2.5 1.5 1.0 4 -2.0 -2.5 -1.0 4.5 5 -2.0 -2.5 -1.5 2.0 6 -2.0 -2.5 1.5 1.5 7 -2.0 -2.5 -1.0 4.5 8 -2.0 -2.5 1.5 2.0 9 -2.0 -2.5 -1.0 4.5 10 -2.0 -2.5 -1.5 2.0 11 -2.0 -2.5 -2.0 1.5 12 -2.0 -2.5 1.5 1.0 FF: 0 0.0 -2.0 -2.0 -2.0 1 0.0 -2.5 -2.5 -2.5 2 0.0 -3.0 -1.5 2.5 3 0.0 -3.5 -2.0 2.0 4 0.0 1.5 -1.0 1.5 5 0.0 1.0 4.5 2.0 6 0.0 0.5 4.0 9.5 7 0.0 1.5 3.5 9.0 8 0.0 1.0 4.5 8.5 9 0.0 1.5 4.0 8.0 10 0.0 1.0 4.5 7.5 11 0.0 0.5 4.0 9.5 12 0.0 0.0 3.5 9.0 TF: 0 8 8 8 8 1 8 1 1 1 2 8 2 4 4 3 8 1 2 4 4 8 4 1 2 5 8 4 4 1 6 8 1 4 4 7 8 4 1 4 8 8 1 4 4 9 8 4 1 4 10 8 4 4 1 11 8 4 4 4 12 8 1 4 4 SS_QG_FSL: 0 1 2 3 SF: 0 0.0 0.0 0.0 0.0 1 0.0 -1.0 1.0 5.0 2 0.0 -2.5 -1.5 2.5 3 0.0 4.0 1.5 2.0 4 0.0 1.5 7.0 4.5 5 0.0 1.0 4.5 12.0 6 0.0 4.0 4.0 9.5 7 0.0 1.5 7.0 9.0 8 0.0 4.0 4.5 8.5 9 0.0 1.5 7.0 8.0 10 0.0 1.0 4.5 12.0 11 0.0 0.5 4.0 9.5 12 0.0 4.0 3.5 9.0 EF: 0 0.0 0.0 0.0 0.0 1 -2.0 -2.5 -3.0 -1.5 2 -2.0 -2.5 -3.0 -3.5 3 -2.0 -2.5 1.5 1.0 4 -2.0 -2.5 -1.0 4.5 5 -2.0 -2.5 -1.5 2.0 6 -2.0 -2.5 1.5 1.5 7 -2.0 -2.5 -1.0 4.5 8 -2.0 -2.5 1.5 2.0 9 -2.0 -2.5 -1.0 4.5 10 -2.0 -2.5 -1.5 2.0 11 -2.0 -2.5 -2.0 1.5 12 -2.0 -2.5 1.5 1.0 FF: 0 0.0 -2.0 -2.0 -2.0 1 0.0 -2.5 -2.5 -2.5 2 0.0 -3.0 -1.5 2.5 3 0.0 -3.5 -2.0 2.0 4 0.0 1.5 -1.0 1.5 5 0.0 1.0 4.5 2.0 6 0.0 0.5 4.0 9.5 7 0.0 1.5 3.5 9.0 8 0.0 1.0 4.5 8.5 9 0.0 1.5 4.0 8.0 10 0.0 1.0 4.5 7.5 11 0.0 0.5 4.0 9.5 12 0.0 0.0 3.5 9.0 TF: 0 8 8 8 8 1 8 1 1 1 2 8 2 4 4 3 8 1 2 4 4 8 4 1 2 5 8 4 4 1 6 8 1 4 4 7 8 4 1 4 8 8 1 4 4 9 8 4 1 4 10 8 4 4 1 11 8 4 4 4 12 8 1 4 4 TEST02: SS_QG_BSQ - Backward score quadratic; SS_QG_BSL - Backward score linear. GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Verify that the BSQ and BSL tables agree. Sequences A and B: 1 G T 2 C A 3 T G 4 A 5 G 6 T 7 A 8 T 9 A 10 G 11 C 12 T SS_QG_BSQ: 0 1 2 3 SB: 0 9.0 4.5 5.0 0.0 1 9.5 5.0 1.5 0.0 2 12.0 5.5 2.0 0.0 3 8.0 8.0 2.5 0.0 4 8.5 4.0 5.0 0.0 5 9.0 4.5 1.0 0.0 6 9.5 5.0 1.5 0.0 7 12.0 5.5 2.0 0.0 8 5.5 8.0 2.5 0.0 9 2.0 2.5 5.0 0.0 10 1.5 -1.5 -2.5 0.0 11 4.0 1.0 -1.0 0.0 12 0.0 0.0 0.0 0.0 EB: 0 2.0 2.5 -2.5 -2.0 1 2.5 -1.0 -2.5 -2.0 2 3.0 -0.5 -2.5 -2.0 3 5.5 0.0 -2.5 -2.0 4 2.0 2.5 -2.5 -2.0 5 2.0 -1.5 -2.5 -2.0 6 2.5 -1.0 -2.5 -2.0 7 3.0 -0.5 -2.5 -2.0 8 5.5 0.0 -2.5 -2.0 9 2.0 2.5 -2.5 -2.0 10 -3.5 -3.0 -2.5 -2.0 11 -1.5 -3.0 -2.5 -2.0 12 0.0 0.0 0.0 0.0 FB: 0 9.0 4.5 1.0 0.0 1 9.5 5.0 1.5 0.0 2 7.5 5.5 2.0 0.0 3 8.0 3.5 2.5 0.0 4 8.5 4.0 0.5 0.0 5 9.0 4.5 1.0 0.0 6 9.5 5.0 1.5 0.0 7 3.0 5.5 2.0 0.0 8 0.5 0.0 2.5 0.0 9 1.0 -2.0 -3.5 0.0 10 1.5 -1.5 -3.0 0.0 11 -2.5 -2.5 -2.5 0.0 12 -2.0 -2.0 -2.0 0.0 TB: 0 4 4 1 8 1 4 4 4 8 2 1 4 4 8 3 4 1 4 8 4 4 4 1 8 5 5 4 4 8 6 4 5 4 8 7 1 4 4 8 8 2 1 4 8 9 2 2 1 8 10 4 4 2 8 11 1 1 1 8 12 8 8 8 8 SS_QG_BSL: 0 1 2 3 SB: 0 9.0 4.5 5.0 0.0 1 9.5 5.0 1.5 0.0 2 12.0 5.5 2.0 0.0 3 8.0 8.0 2.5 0.0 4 8.5 4.0 5.0 0.0 5 9.0 4.5 1.0 0.0 6 9.5 5.0 1.5 0.0 7 12.0 5.5 2.0 0.0 8 5.5 8.0 2.5 0.0 9 2.0 2.5 5.0 0.0 10 1.5 -1.5 -2.5 0.0 11 4.0 1.0 -1.0 0.0 12 0.0 0.0 0.0 0.0 EB: 0 2.0 2.5 -2.5 -2.0 1 2.5 -1.0 -2.5 -2.0 2 3.0 -0.5 -2.5 -2.0 3 5.5 0.0 -2.5 -2.0 4 2.0 2.5 -2.5 -2.0 5 2.0 -1.5 -2.5 -2.0 6 2.5 -1.0 -2.5 -2.0 7 3.0 -0.5 -2.5 -2.0 8 5.5 0.0 -2.5 -2.0 9 2.0 2.5 -2.5 -2.0 10 -3.5 -3.0 -2.5 -2.0 11 -1.5 -3.0 -2.5 -2.0 12 0.0 0.0 0.0 0.0 FB: 0 9.0 4.5 1.0 0.0 1 9.5 5.0 1.5 0.0 2 7.5 5.5 2.0 0.0 3 8.0 3.5 2.5 0.0 4 8.5 4.0 0.5 0.0 5 9.0 4.5 1.0 0.0 6 9.5 5.0 1.5 0.0 7 3.0 5.5 2.0 0.0 8 0.5 0.0 2.5 0.0 9 1.0 -2.0 -3.5 0.0 10 1.5 -1.5 -3.0 0.0 11 -2.5 -2.5 -2.5 0.0 12 -2.0 -2.0 -2.0 0.0 TB: 0 4 4 1 8 1 4 4 4 8 2 1 4 4 8 3 4 1 4 8 4 4 4 1 8 5 5 4 4 8 6 4 5 4 8 7 1 4 4 8 8 2 1 4 8 9 2 2 1 8 10 4 4 2 8 11 1 1 1 8 12 8 8 8 8 TEST03: SS_QG_FSQ - Forward score quadratic; SS_QG_FSL - Forward score linear; GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Verify that the FSQ and FSL tables agree. Sequences A and B: 1 G G 2 C G 3 T G 4 T Matching scores: 0 0.0 0.0 0.0 0.0 0.0 1 0.0 5.0 5.0 5.0 -1.0 2 0.0 -5.0 -5.0 -5.0 -3.0 3 0.0 -1.0 -1.0 -1.0 4.0 SS_QG_FSQ: 0 1 2 3 4 SF: 0 0.0 0.0 0.0 0.0 0.0 1 0.0 5.0 5.0 5.0 2.5 2 0.0 2.5 2.5 2.5 2.0 3 0.0 2.0 2.0 2.0 6.5 EF: 0 0.0 0.0 0.0 0.0 0.0 1 -2.0 -2.5 2.5 2.5 2.5 2 -2.0 -2.5 0.0 0.0 0.0 3 -2.0 -2.5 -0.5 -0.5 -0.5 FF: 0 0.0 -2.0 -2.0 -2.0 -2.0 1 0.0 -2.5 -2.5 -2.5 -2.5 2 0.0 2.5 2.5 2.5 0.0 3 0.0 2.0 2.0 2.0 -0.5 TF: 0 8 8 8 8 8 1 8 1 1 1 2 2 8 4 4 4 1 3 8 4 4 4 1 SS_QG_FSL: 0 1 2 3 4 SF: 0 0.0 0.0 0.0 0.0 0.0 1 0.0 5.0 5.0 5.0 2.5 2 0.0 2.5 2.5 2.5 2.0 3 0.0 2.0 2.0 2.0 6.5 EF: 0 0.0 0.0 0.0 0.0 0.0 1 -2.0 -2.5 2.5 2.5 2.5 2 -2.0 -2.5 0.0 0.0 0.0 3 -2.0 -2.5 -0.5 -0.5 -0.5 FF: 0 0.0 -2.0 -2.0 -2.0 -2.0 1 0.0 -2.5 -2.5 -2.5 -2.5 2 0.0 2.5 2.5 2.5 0.0 3 0.0 2.0 2.0 2.0 -0.5 TF: 0 8 8 8 8 8 1 8 1 1 1 2 2 8 4 4 4 1 3 8 4 4 4 1 TEST04: SS_QG_BSQ - Backward score quadratic; SS_QG_BSL - Backward score linear. GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Verify that the BSQ and BSL tables agree. Sequences A and B: 1 G G 2 C G 3 T G 4 T SS_QG_BSQ: 0 1 2 3 4 SB: 0 3.5 4.0 6.5 1.0 0.0 1 -2.0 -1.5 -1.0 1.5 0.0 2 0.5 1.0 1.5 4.0 0.0 3 0.0 0.0 0.0 0.0 0.0 EB: 0 3.5 4.0 -1.5 -2.5 -2.0 1 -2.0 -1.5 -1.0 -2.5 -2.0 2 0.5 1.0 1.5 -2.5 -2.0 3 0.0 0.0 0.0 0.0 0.0 FB: 0 -2.5 -2.0 -1.5 1.0 0.0 1 -2.0 -1.5 -1.0 1.5 0.0 2 -2.5 -2.5 -2.5 -2.5 0.0 3 -2.0 -2.0 -2.0 -2.0 0.0 TB: 0 3 3 1 4 8 1 6 6 7 4 8 2 2 2 2 1 8 3 8 8 8 8 8 SS_QG_BSL: 0 1 2 3 4 SB: 0 3.5 4.0 6.5 1.0 0.0 1 -2.0 -1.5 -1.0 1.5 0.0 2 0.5 1.0 1.5 4.0 0.0 3 0.0 0.0 0.0 0.0 0.0 EB: 0 3.5 4.0 -1.5 -2.5 -2.0 1 -2.0 -1.5 -1.0 -2.5 -2.0 2 0.5 1.0 1.5 -2.5 -2.0 3 0.0 0.0 0.0 0.0 0.0 FB: 0 -2.5 -2.0 -1.5 1.0 0.0 1 -2.0 -1.5 -1.0 1.5 0.0 2 -2.5 -2.5 -2.5 -2.5 0.0 3 -2.0 -2.0 -2.0 -2.0 0.0 TB: 0 3 3 1 4 8 1 6 6 7 4 8 2 2 2 2 1 8 3 8 8 8 8 8 TEST05: SS_QG_BSQ - Backward score quadratic; SS_QG_FSQ - Forward score quadratic. GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Verify that the FSQ and (reversed) BSQ tables agree. Sequences A and B: 1 G G 2 C G 3 T G 4 T SS_QG_FSQ: 0 1 2 3 4 SF: 0 0.0 0.0 0.0 0.0 0.0 1 0.0 5.0 5.0 5.0 2.5 2 0.0 2.5 2.5 2.5 2.0 3 0.0 2.0 2.0 2.0 6.5 EF: 0 0.0 0.0 0.0 0.0 0.0 1 -2.0 -2.5 2.5 2.5 2.5 2 -2.0 -2.5 0.0 0.0 0.0 3 -2.0 -2.5 -0.5 -0.5 -0.5 FF: 0 0.0 -2.0 -2.0 -2.0 -2.0 1 0.0 -2.5 -2.5 -2.5 -2.5 2 0.0 2.5 2.5 2.5 0.0 3 0.0 2.0 2.0 2.0 -0.5 TF: 0 8 8 8 8 8 1 8 1 1 1 2 2 8 4 4 4 1 3 8 4 4 4 1 Reversed sequences A and B: 1 T T 2 C G 3 G G 4 G SS_QG_BSQ: (The tables are printed in reverse order) 4 3 2 1 0 SB: 3 0.0 0.0 0.0 0.0 0.0 2 0.0 5.0 5.0 5.0 2.5 1 0.0 2.5 2.5 2.5 2.0 0 0.0 2.0 2.0 2.0 6.5 EB: 3 0.0 0.0 0.0 0.0 0.0 2 -2.0 -2.5 2.5 2.5 2.5 1 -2.0 -2.5 0.0 0.0 0.0 0 -2.0 -2.5 -0.5 -0.5 -0.5 FB: 3 0.0 -2.0 -2.0 -2.0 -2.0 2 0.0 -2.5 -2.5 -2.5 -2.5 1 0.0 2.5 2.5 2.5 0.0 0 0.0 2.0 2.0 2.0 -0.5 TB: 3 8 8 8 8 8 2 8 1 1 1 2 1 8 4 4 4 1 0 8 4 4 4 1 TEST07: SS_QG_FSQ - forward score quadratic SS_QG_FOQ - forward optimal score quadratic SS_QG_FPQ - forward path quadratic GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Sequences A and B: 1 G T 2 C A 3 T G 4 A 5 G 6 T 7 A 8 T 9 A 10 G 11 C 12 T SS_QG_FOQ reports optimal matching score is 12.0000 I2 = 10 J2 = 3 Matching path: 1 7 0 2 8 1 3 9 2 4 10 3 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 8 T = T 1 4.00 4.00 9 A = A 2 3.00 7.00 10 G = G 3 5.00 12.00 TEST08: SS_QG_BSQ - backward score quadratic SS_QG_BOQ - backward optimal score quadratic SS_QG_BPQ - backward path quadratic GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Compare path and score with FSQ/FPQ computation. Sequences A and B: 1 G T 2 C A 3 T G 4 A 5 G 6 T 7 A 8 T 9 A 10 G 11 C 12 T SS_QG_BOQ reports optimal matching score is 12.0000 I1 = 7 J1 = 0 Matching path: 1 7 0 2 8 1 3 9 2 4 10 3 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 8 T = T 1 4.00 4.00 9 A = A 2 3.00 7.00 10 G = G 3 5.00 12.00 TEST09: SS_QG_RPL - path routine; GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Verify that RPL agrees with FSQ/FPQ and BSQ/BPQ. Sequences A and B: 1 G T 2 C A 3 T G 4 A 5 G 6 T 7 A 8 T 9 A 10 G 11 C 12 T Matching path: 1 2 0 2 3 1 3 4 2 4 5 3 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 3 T = T 1 4.00 4.00 4 A = A 2 3.00 7.00 5 G = G 3 5.00 12.00 TEST12: SS_QG_FSQ - forward score quadratic; SS_QG_FOQ - forward optimal score quadratic SS_QG_FPQ - Forward path quadratic. GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. SS_QG_FOQ reports optimal matching score is 249.500 I2 = 60 J2 = 59 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 M = M 1 8.00 8.00 2 M = M 2 8.00 16.00 3 A = A 3 3.00 19.00 4 A = A 4 3.00 22.00 5 E = E 5 5.00 27.00 6 A = A 6 3.00 30.00 7 G = G 7 5.00 35.00 8 G = G 8 5.00 40.00 9 E | -2.50 37.50 10 E | -0.50 37.00 11 G | -0.50 36.50 12 G | -0.50 36.00 13 P = P 9 6.00 42.00 14 V = V 10 5.00 47.00 15 T = T 11 4.00 51.00 16 A = A 12 3.00 54.00 17 G = G 13 5.00 59.00 18 A = A 14 3.00 62.00 19 A = A 15 3.00 65.00 20 G = G 16 5.00 70.00 21 G = G 17 5.00 75.00 22 G = G 18 5.00 80.00 23 A = A 19 3.00 83.00 24 A = A 20 3.00 86.00 | C 21 -2.50 83.50 | C 22 -0.50 83.00 | C 23 -0.50 82.50 25 A = A 24 3.00 85.50 26 A = A 25 3.00 88.50 27 S = S 26 3.00 91.50 28 G = G 27 5.00 96.50 29 A = A 28 3.00 99.50 30 Y = Y 29 8.00 107.50 31 P = P 30 6.00 113.50 32 A = A 31 3.00 116.50 33 V = V 32 5.00 121.50 34 C = C 33 9.00 130.50 35 R = R 34 6.00 136.50 36 V = V 35 5.00 141.50 37 K = K 36 5.00 146.50 38 I = I 37 6.00 152.50 39 P = P 38 6.00 158.50 40 A = A 39 3.00 161.50 41 A = A 40 3.00 164.50 42 L = L 41 5.00 169.50 43 P = P 42 6.00 175.50 44 V = V 43 5.00 180.50 45 A = A 44 3.00 183.50 46 A = A 45 3.00 186.50 47 A = A 46 3.00 189.50 48 A = A 47 3.00 192.50 49 P = P 48 6.00 198.50 50 F = F 49 8.00 206.50 51 P = P 50 6.00 212.50 52 G = G 51 5.00 217.50 53 L = L 52 5.00 222.50 54 A = A 53 3.00 225.50 55 E = E 54 5.00 230.50 56 A = A 55 3.00 233.50 57 G = G 56 5.00 238.50 58 V = V 57 5.00 243.50 59 A = A 58 3.00 246.50 60 A = A 59 3.00 249.50 TEST13: SS_QG_RPL - path routine; GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Compare with FSQ/FPQ calculation. Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 M = M 1 8.00 8.00 2 M = M 2 8.00 16.00 3 A = A 3 3.00 19.00 4 A = A 4 3.00 22.00 5 E = E 5 5.00 27.00 6 A = A 6 3.00 30.00 7 G | -2.50 27.50 8 G | -0.50 27.00 9 E | -0.50 26.50 10 E | -0.50 26.00 11 G = G 7 5.00 31.00 12 G = G 8 5.00 36.00 13 P = P 9 6.00 42.00 14 V = V 10 5.00 47.00 15 T = T 11 4.00 51.00 16 A = A 12 3.00 54.00 17 G = G 13 5.00 59.00 18 A = A 14 3.00 62.00 19 A = A 15 3.00 65.00 20 G = G 16 5.00 70.00 21 G = G 17 5.00 75.00 22 G = G 18 5.00 80.00 23 A = A 19 3.00 83.00 24 A = A 20 3.00 86.00 | C 21 -2.50 83.50 | C 22 -0.50 83.00 | C 23 -0.50 82.50 25 A = A 24 3.00 85.50 26 A = A 25 3.00 88.50 27 S = S 26 3.00 91.50 28 G = G 27 5.00 96.50 29 A = A 28 3.00 99.50 30 Y = Y 29 8.00 107.50 31 P = P 30 6.00 113.50 32 A = A 31 3.00 116.50 33 V = V 32 5.00 121.50 34 C = C 33 9.00 130.50 35 R = R 34 6.00 136.50 36 V = V 35 5.00 141.50 37 K = K 36 5.00 146.50 38 I = I 37 6.00 152.50 39 P = P 38 6.00 158.50 40 A = A 39 3.00 161.50 41 A = A 40 3.00 164.50 42 L = L 41 5.00 169.50 43 P = P 42 6.00 175.50 44 V = V 43 5.00 180.50 45 A = A 44 3.00 183.50 46 A = A 45 3.00 186.50 47 A = A 46 3.00 189.50 48 A = A 47 3.00 192.50 49 P = P 48 6.00 198.50 50 F = F 49 8.00 206.50 51 P = P 50 6.00 212.50 52 G = G 51 5.00 217.50 53 L = L 52 5.00 222.50 54 A = A 53 3.00 225.50 55 E = E 54 5.00 230.50 56 A = A 55 3.00 233.50 57 G = G 56 5.00 238.50 58 V = V 57 5.00 243.50 59 A = A 58 3.00 246.50 60 A = A 59 3.00 249.50 TEST14: SS_QG_FSQ - forward score quadratic; SS_QG_FOQ - forward optimal score quadratic SS_QG_FSL - Forward score linear; GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by SIMPLE_SCORE. Verify that FSQ and FSL agree. Sequences A and B: 1 A A 2 G A 3 T G 4 A 5 C Matching scores: 0 0.0 0.0 0.0 0.0 1 0.0 2.0 2.0 -1.0 2 0.0 -1.0 -1.0 2.0 3 0.0 -1.0 -1.0 -1.0 4 0.0 2.0 2.0 -1.0 5 0.0 -1.0 -1.0 -1.0 SS_QG_FSQ: 0 1 2 3 SF: 0 0.0 0.0 0.0 0.0 1 0.0 2.0 2.0 -0.5 2 0.0 -0.5 1.0 4.0 3 0.0 -1.0 -1.0 1.5 4 0.0 2.0 1.0 1.0 5 0.0 -0.5 1.0 0.5 EF: 0 0.0 0.0 0.0 0.0 1 -2.0 -2.5 -0.5 -0.5 2 -2.0 -2.5 -3.0 -1.5 3 -2.0 -2.5 -3.0 -3.5 4 -2.0 -2.5 -0.5 -1.0 5 -2.0 -2.5 -3.0 -1.5 FF: 0 0.0 -2.0 -2.0 -2.0 1 0.0 -2.5 -2.5 -2.5 2 0.0 -0.5 -0.5 -3.0 3 0.0 -1.0 -1.0 1.5 4 0.0 -1.5 -1.5 1.0 5 0.0 -0.5 -1.5 0.5 TF: 0 8 8 8 8 1 8 1 1 2 2 8 4 1 1 3 8 5 4 4 4 8 1 1 4 5 8 4 1 4 SS_QG_FSL: 0 1 2 3 SF: 0 0.0 0.0 0.0 0.0 1 0.0 2.0 2.0 -0.5 2 0.0 -0.5 1.0 4.0 3 0.0 -1.0 -1.0 1.5 4 0.0 2.0 1.0 1.0 5 0.0 -0.5 1.0 0.5 EF: 0 0.0 0.0 0.0 0.0 1 -2.0 -2.5 -0.5 -0.5 2 -2.0 -2.5 -3.0 -1.5 3 -2.0 -2.5 -3.0 -3.5 4 -2.0 -2.5 -0.5 -1.0 5 -2.0 -2.5 -3.0 -1.5 FF: 0 0.0 -2.0 -2.0 -2.0 1 0.0 -2.5 -2.5 -2.5 2 0.0 -0.5 -0.5 -3.0 3 0.0 -1.0 -1.0 1.5 4 0.0 -1.5 -1.5 1.0 5 0.0 -0.5 -1.5 0.5 TF: 0 8 8 8 8 1 8 1 1 2 2 8 4 1 1 3 8 5 4 4 4 8 1 1 4 5 8 4 1 4 TEST15: SS_QG_BSQ - Backward score quadratic; SS_QG_BSL - Backward score linear; GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by SIMPLE_SCORE. Compare BSQ and BSL results. Sequences A and B: 1 A A 2 G A 3 T G 4 A 5 C SS_QG_BSQ: 0 1 2 3 SF: 0 1.5 4.0 -0.5 0.0 1 -1.0 -0.5 2.0 0.0 2 0.0 -1.5 -1.0 0.0 3 1.0 1.0 -1.0 0.0 4 -1.0 -1.0 -1.0 0.0 5 0.0 0.0 0.0 0.0 EF: 0 1.5 -3.0 -2.5 -2.0 1 -1.0 -0.5 -2.5 -2.0 2 -3.5 -3.0 -2.5 -2.0 3 -1.5 -3.0 -2.5 -2.0 4 -3.5 -3.0 -2.5 -2.0 5 0.0 0.0 0.0 0.0 FF: 0 -2.5 -2.5 -0.5 0.0 1 -2.0 -2.0 -3.5 0.0 2 -1.5 -1.5 -3.5 0.0 3 -3.0 -3.0 -3.0 0.0 4 -2.5 -2.5 -2.5 0.0 5 -2.0 -2.0 -2.0 0.0 TF: 0 3 1 4 8 1 2 2 1 8 2 1 4 1 8 3 1 1 1 8 4 1 1 1 8 5 8 8 8 8 SS_QG_BSL: 0 1 2 3 SF: 0 1.5 4.0 -0.5 0.0 1 -1.0 -0.5 2.0 0.0 2 0.0 -1.5 -1.0 0.0 3 1.0 1.0 -1.0 0.0 4 -1.0 -1.0 -1.0 0.0 5 0.0 0.0 0.0 0.0 EF: 0 1.5 -3.0 -2.5 -2.0 1 -1.0 -0.5 -2.5 -2.0 2 -3.5 -3.0 -2.5 -2.0 3 -1.5 -3.0 -2.5 -2.0 4 -3.5 -3.0 -2.5 -2.0 5 0.0 0.0 0.0 0.0 FF: 0 -2.5 -2.5 -0.5 0.0 1 -2.0 -2.0 -3.5 0.0 2 -1.5 -1.5 -3.5 0.0 3 -3.0 -3.0 -3.0 0.0 4 -2.5 -2.5 -2.5 0.0 5 -2.0 -2.0 -2.0 0.0 TF: 0 3 1 4 8 1 2 2 1 8 2 1 4 1 8 3 1 1 1 8 4 1 1 1 8 5 8 8 8 8 TEST16: SS_QG_FSQ - forward score quadratic SS_QG_FOQ - forward optimal score quadratic SS_QG_FPQ - forward path quadratic GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by SIMPLE_SCORE. Sequences A and B: 1 A A 2 G A 3 T G 4 A 5 C SS_QG_FSQ: 0 1 2 3 SF: 0 0.0 0.0 0.0 0.0 1 0.0 2.0 2.0 -0.5 2 0.0 -0.5 1.0 4.0 3 0.0 -1.0 -1.0 1.5 4 0.0 2.0 1.0 1.0 5 0.0 -0.5 1.0 0.5 EF: 0 0.0 0.0 0.0 0.0 1 -2.0 -2.5 -0.5 -0.5 2 -2.0 -2.5 -3.0 -1.5 3 -2.0 -2.5 -3.0 -3.5 4 -2.0 -2.5 -0.5 -1.0 5 -2.0 -2.5 -3.0 -1.5 FF: 0 0.0 -2.0 -2.0 -2.0 1 0.0 -2.5 -2.5 -2.5 2 0.0 -0.5 -0.5 -3.0 3 0.0 -1.0 -1.0 1.5 4 0.0 -1.5 -1.5 1.0 5 0.0 -0.5 -1.5 0.5 TF: 0 8 8 8 8 1 8 1 1 2 2 8 4 1 1 3 8 5 4 4 4 8 1 1 4 5 8 4 1 4 SS_QG_FOQ reports optimal matching score is 4.00000 I2 = 2 J2 = 3 Matching path: 1 0 1 2 1 2 3 2 3 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 A = A 2 2.00 2.00 2 G = G 3 2.00 4.00 TEST165: SS_QG_BSQ - backward score quadratic SS_QG_BOQ - backward optimal score quadratic SS_QG_BPQ - backward path quadratic GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by SIMPLE_SCORE. Sequences A and B: 1 A A 2 G A 3 T G 4 A 5 C SS_QG_BSQ: 0 1 2 3 SB: 0 1.5 4.0 -0.5 0.0 1 -1.0 -0.5 2.0 0.0 2 0.0 -1.5 -1.0 0.0 3 1.0 1.0 -1.0 0.0 4 -1.0 -1.0 -1.0 0.0 5 0.0 0.0 0.0 0.0 EB: 0 1.5 -3.0 -2.5 -2.0 1 -1.0 -0.5 -2.5 -2.0 2 -3.5 -3.0 -2.5 -2.0 3 -1.5 -3.0 -2.5 -2.0 4 -3.5 -3.0 -2.5 -2.0 5 0.0 0.0 0.0 0.0 FB: 0 -2.5 -2.5 -0.5 0.0 1 -2.0 -2.0 -3.5 0.0 2 -1.5 -1.5 -3.5 0.0 3 -3.0 -3.0 -3.0 0.0 4 -2.5 -2.5 -2.5 0.0 5 -2.0 -2.0 -2.0 0.0 TB: 0 3 1 4 8 1 2 2 1 8 2 1 4 1 8 3 1 1 1 8 4 1 1 1 8 5 8 8 8 8 SS_QG_BOQ reports optimal matching score is 4.00000 I1 = 0 J1 = 1 Matching path: 1 0 1 2 1 2 3 2 3 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 A = A 2 2.00 2.00 2 G = G 3 2.00 4.00 TEST17: SS_QG_RPL - recursive path linear GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by SIMPLE_SCORE. Compare with FPQ results. Sequences A and B: 1 A A 2 G A 3 T G 4 A 5 C Matching path: 1 0 1 2 1 2 3 2 3 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 A = A 2 2.00 2.00 2 G = G 3 2.00 4.00 TEST18: SS_QG_RPL - recursive path linear GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by SIMPLE_SCORE. We simply switched the two sequences. Compare with unswitched results. Sequences A and B: 1 A A 2 A G 3 G T 4 A 5 C Matching path: 1 1 0 2 2 1 3 3 2 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 2 A = A 1 2.00 2.00 3 G = G 2 2.00 4.00 TEST20: SS_QG_FSQ - forward score quadratic; SS_QG_FOQ - forward optimal score quadratic SS_QG_FPQ - forward path quadratic; SS_QG_RPL - recursive path linear; GAP_OPEN penalty = -2.00000 GAP_EXTEND penalty = -0.500000 Matching scores by PAM120_SCORE. Compare the score computed by FSQ/FPQ with the score associated with the path determined by RPL. If the scores don't match, the paths differ, and presumably, the RPL algorithm has failed. The test is carried out by comparing a fixed sequence with many "mutated" variations. Using a random number seed of ISEED = 1256839993 Test Quadratic Linear 1 39.0000 39.0000 2 52.0000 52.0000 3 55.0000 55.0000 4 52.5000 52.5000 5 55.0000 55.0000 6 25.5000 25.5000 7 47.0000 47.0000 8 58.0000 58.0000 9 54.5000 54.5000 10 52.5000 52.5000 Details for sample test number 10 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 1 5.00 5.00 2 C = C 2 9.00 14.00 | W 3 -2.50 11.50 3 T = T 4 4.00 15.50 4 G = G 5 5.00 20.50 5 A = A 6 3.00 23.50 6 T = T 7 4.00 27.50 7 A = A 8 3.00 30.50 | I 9 -2.50 28.00 | P 10 -0.50 27.50 8 T = T 11 4.00 31.50 9 A = A 12 3.00 34.50 10 G = G 13 5.00 39.50 11 C = C 14 9.00 48.50 12 T = T 15 4.00 52.50 11 26.0000 26.0000 12 32.0000 32.0000 13 30.5000 30.5000 14 43.0000 43.0000 15 31.5000 31.5000 16 25.0000 25.0000 17 45.0000 45.0000 18 51.0000 51.0000 19 53.0000 53.0000 20 37.5000 37.5000 Details for sample test number 20 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 1 5.00 5.00 2 C = C 2 9.00 14.00 3 T = T 3 4.00 18.00 4 G = G 4 5.00 23.00 5 A = A 5 3.00 26.00 6 T = T 6 4.00 30.00 7 A = A 7 3.00 33.00 | P 8 -2.50 30.50 8 T = T 9 4.00 34.50 9 A = A 10 3.00 37.50 21 29.0000 29.0000 22 54.5000 54.5000 23 42.5000 42.5000 24 52.0000 52.0000 25 52.5000 52.5000 26 34.5000 34.5000 27 29.0000 29.0000 28 47.0000 47.0000 29 25.0000 25.0000 30 42.0000 42.0000 Details for sample test number 30 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 1 5.00 5.00 2 C = C 2 9.00 14.00 3 T - C 3 -3.00 11.00 4 G = G 4 5.00 16.00 5 A = A 5 3.00 19.00 6 T = T 6 4.00 23.00 7 A = A 7 3.00 26.00 8 T | -2.50 23.50 | W 8 -2.50 21.00 9 A = A 9 3.00 24.00 10 G = G 10 5.00 29.00 11 C = C 11 9.00 38.00 12 T = T 12 4.00 42.00 31 39.0000 39.0000 32 47.5000 47.5000 33 43.0000 43.0000 34 40.5000 40.5000 35 31.0000 31.0000 36 41.0000 41.0000 37 51.0000 51.0000 38 25.0000 25.0000 39 55.0000 55.0000 40 58.0000 58.0000 Details for sample test number 40 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 1 5.00 5.00 2 C = C 2 9.00 14.00 3 T = T 3 4.00 18.00 4 G = G 4 5.00 23.00 5 A = A 5 3.00 26.00 6 T = T 6 4.00 30.00 7 A = A 7 3.00 33.00 8 T = T 8 4.00 37.00 9 A = A 9 3.00 40.00 10 G = G 10 5.00 45.00 11 C = C 11 9.00 54.00 12 T = T 12 4.00 58.00 41 55.0000 55.0000 42 41.5000 41.5000 43 40.5000 40.5000 44 43.5000 43.5000 45 36.5000 36.5000 46 7.00000 7.00000 47 52.0000 52.0000 48 42.5000 42.5000 49 46.0000 46.0000 50 31.5000 31.5000 Details for sample test number 50 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 1 5.00 5.00 2 C = C 2 9.00 14.00 | E 3 -2.50 11.50 | B 4 -0.50 11.00 3 T - P 5 -1.00 10.00 4 G = G 6 5.00 15.00 5 A | -2.50 12.50 6 T = T 7 4.00 16.50 7 A = A 8 3.00 19.50 8 T = T 9 4.00 23.50 9 A = A 10 3.00 26.50 10 G = G 11 5.00 31.50 51 38.5000 38.5000 52 49.5000 49.5000 53 45.0000 45.0000 54 24.0000 24.0000 55 46.0000 46.0000 56 28.5000 28.5000 57 50.0000 50.0000 58 25.0000 25.0000 59 40.5000 40.5000 60 51.5000 51.5000 Details for sample test number 60 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 1 5.00 5.00 2 C = C 2 9.00 14.00 3 T = T 3 4.00 18.00 4 G = G 4 5.00 23.00 5 A = A 5 3.00 26.00 6 T = T 6 4.00 30.00 7 A = A 7 3.00 33.00 8 T = T 8 4.00 37.00 9 A = A 9 3.00 40.00 10 G = G 10 5.00 45.00 11 C = C 11 9.00 54.00 | Y 12 -2.50 51.50 61 52.5000 52.5000 62 44.5000 44.5000 63 11.0000 11.0000 64 54.5000 54.5000 65 56.0000 56.0000 66 37.0000 37.0000 67 54.5000 54.5000 68 51.0000 51.0000 69 42.5000 42.5000 70 31.0000 31.0000 Details for sample test number 70 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 1 5.00 5.00 2 C = C 2 9.00 14.00 3 T | -2.50 11.50 4 G = G 3 5.00 16.50 5 A | -2.50 14.00 6 T = T 4 4.00 18.00 7 A = A 5 3.00 21.00 8 T - I 6 0.00 21.00 9 A | -2.50 18.50 10 G | -0.50 18.00 11 C = C 7 9.00 27.00 12 T = T 8 4.00 31.00 71 55.5000 55.5000 72 50.5000 50.5000 73 34.0000 34.0000 74 51.0000 51.0000 75 42.0000 42.0000 76 34.5000 34.5000 77 58.0000 58.0000 78 55.5000 55.5000 79 33.5000 33.5000 80 31.0000 31.0000 Details for sample test number 80 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 4 G = G 1 5.00 5.00 | K 2 -2.50 2.50 5 A = A 3 3.00 5.50 6 T = T 4 4.00 9.50 7 A = A 5 3.00 12.50 8 T = T 6 4.00 16.50 9 A = A 7 3.00 19.50 10 G = G 8 5.00 24.50 11 C = C 9 9.00 33.50 | C 10 -2.50 31.00 81 46.0000 46.0000 82 50.0000 50.0000 83 40.5000 40.5000 84 37.0000 37.0000 85 49.0000 49.0000 86 12.0000 12.0000 87 48.0000 48.0000 88 46.0000 46.0000 89 40.0000 40.0000 90 39.0000 39.0000 Details for sample test number 90 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 1 5.00 5.00 2 C = C 2 9.00 14.00 3 T = T 3 4.00 18.00 4 G = G 4 5.00 23.00 5 A = A 5 3.00 26.00 6 T = T 6 4.00 30.00 7 A | -2.50 27.50 8 T | -0.50 27.00 9 A | -0.50 26.50 10 G | -0.50 26.00 11 C = C 7 9.00 35.00 12 T = T 8 4.00 39.00 91 30.0000 30.0000 92 45.0000 45.0000 93 23.5000 23.5000 94 23.0000 23.0000 95 48.0000 48.0000 96 36.5000 36.5000 97 41.0000 41.0000 98 48.0000 48.0000 99 4.00000 4.00000 100 45.5000 45.5000 Details for sample test number 100 Sequence/sequence matching, Affine gap penalty: # A B # Increm Score 0.00 1 G = G 1 5.00 5.00 2 C = C 2 9.00 14.00 3 T = T 3 4.00 18.00 4 G | -2.50 15.50 | W 4 -2.50 13.00 5 A = A 5 3.00 16.00 6 T = T 6 4.00 20.00 7 A = A 7 3.00 23.00 8 T = T 8 4.00 27.00 9 A = A 9 3.00 30.00 10 G = G 10 5.00 35.00 | F 11 -2.50 32.50 11 C = C 12 9.00 41.50 12 T = T 13 4.00 45.50 Number of score agreements = 100 Number of score disagreements = 0 SS_QG_ALIGN_PRB Normal end of execution. December 29 2007 9:08:40.397 AM