% SAM: /projects/compbio/bin/i686/hmmscore v3.3.2 (February, 2001) compiled 06/24/02_10:50:12 % (c) 1992-2001 Regents of the University of California, Santa Cruz % % Sequence Alignment and Modeling Software System % http://www.cse.ucsc.edu/research/compbio/sam.html % % ----------------- Citations (SAM, SAM-T99, HMMs) -------------------- % R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: % Extension and analysis of the basic method, CABIOS 12:95-107, 1996. % K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting % remote protein homologies, Bioinformatics 14(10):846-856, 1998. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % stridefoo.1.YGR036C.t2k-100-30-stride-ebghtl Host: cc50 Fri Nov 8 19:32:36 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR036C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.2ds % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR036C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR036C.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 240 nodes, 165.60 seconds % % Sequence scores selected if better than: % E-value (Emax 4.0e+01) (select_score=4) % % Simple: NLL-NULL using FIM probabilities % Reverse: NLL-NULL for the reverse sequence NULL model % Calculated when Simple < simple_threshold (0.00) % E-value on N (=7316) sequences: % N / (1 + exp(-(lambda(=2.0448) * Reverse)^tau(=0.7659))) % Calculated when Simple < simple_threshold (0.00) % Rescale E-values or use -dbsize for multiple scoring runs. % Scores sorted by E-value, best first % % Sequence ID Length Simple Reverse E-value X count 1d2tA 231 -70.07 -46.45 4.54e-11 1qi9A 556 -62.11 -36.34 1.24e-08 1vns 609 -58.46 -32.49 1.15e-07 1vnc 609 -58.41 -32.39 1.22e-07 1qhbA 596 -57.10 -28.59 1.17e-06 1e19A 314 -37.44 -14.63 9.97e-03 1li5A 461 -34.75 -11.46 1.00e-01 1avpA 204 -31.00 -9.52 4.43e-01 1b7bA 310 -31.28 -9.29 5.27e-01 1s01 283 -29.65 -8.64 8.84e-01 1h6kA 757 -36.03 -8.50 9.86e-01 1h2vC 771 -37.07 -8.20 1.26e+00 1kzhA 555 -32.66 -7.98 1.50e+00 1be3D 241 -33.96 -7.70 1.89e+00 1khdA 345 -29.67 -7.33 2.57e+00 1kpkA 473 -38.40 -7.25 2.74e+00 1jw9B 249 -27.70 -7.25 2.75e+00 1bccD 241 -33.63 -7.18 2.92e+00 1be3C 379 -36.92 -6.61 4.70e+00 1ie9A 259 -29.87 -6.47 5.32e+00 1jplA 171 -29.72 -6.30 6.15e+00 5ldh 334 -29.36 -6.30 6.16e+00 1k7qA 479 -28.31 -6.14 7.05e+00 1lqpA 135 -26.10 -6.07 7.50e+00 1occG 84 -29.34 -6.04 7.66e+00 1alu 186 -29.99 -6.04 7.67e+00 1db1A 259 -30.17 -5.94 8.36e+00 1fqyA 269 -32.75 -5.92 8.53e+00 1m55A 197 -26.57 -5.84 9.12e+00 1sup 275 -26.62 -5.71 1.03e+01 1jbuH 254 -25.53 -5.64 1.09e+01 1il6 185 -29.03 -5.63 1.10e+01 1lw6E 281 -26.56 -5.62 1.11e+01 6prcM 323 -35.91 -5.61 1.12e+01 1dxrM 323 -35.38 -5.59 1.14e+01 1danH 254 -25.53 -5.52 1.21e+01 1ewqA 765 -30.49 -5.46 1.28e+01 1gu9A 177 -28.92 -5.44 1.30e+01 1go7P 462 -27.42 -5.40 1.36e+01 1kncA 177 -29.89 -5.20 1.61e+01 1qcrD 75 -27.98 -5.16 1.68e+01 1a6dA 545 -31.22 -5.06 1.83e+01 2abd 86 -24.57 -5.06 1.83e+01 1a0fA 201 -27.81 -5.03 1.88e+01 1bjt 793 -30.27 -5.01 1.92e+01 1k7gA 479 -27.28 -4.98 1.96e+01 1ixh 321 -26.13 -4.96 2.00e+01 1fa0A 537 -29.32 -4.96 2.00e+01 1lr0A 129 -25.67 -4.93 2.06e+01 1gg3A 279 -29.01 -4.93 2.06e+01 1flcA 432 -26.85 -4.90 2.12e+01 1sbp 310 -26.89 -4.90 2.12e+01 1l7vA 326 -40.09 -4.88 2.15e+01 2occG 84 -28.15 -4.85 2.22e+01 1hdmA 201 -25.18 -4.79 2.34e+01 1go8P 462 -26.80 -4.76 2.40e+01 1fe8A 196 -24.65 -4.69 2.55e+01 4rnpA 883 -30.78 -4.69 2.57e+01 1tlfA 301 -25.49 -4.68 2.60e+01 1k7iA 479 -26.72 -4.61 2.75e+01 1lqtA 456 -27.20 -4.61 2.77e+01 1k47A 337 -27.66 -4.61 2.77e+01 1fftC 204 -31.74 -4.59 2.81e+01 1sqc 631 -31.09 -4.59 2.82e+01 1pymA 295 -27.23 -4.58 2.85e+01 1ekeA 230 -29.13 -4.57 2.87e+01 1qd1A 325 -25.92 -4.55 2.91e+01 1a8q 274 -26.51 -4.54 2.95e+01 2ezk 99 -23.73 -4.51 3.04e+01 1zymA 258 -27.23 -4.48 3.11e+01 2ezl 99 -23.79 -4.48 3.12e+01 1egdA 396 -28.79 -4.45 3.19e+01 3fruA 269 -26.37 -4.43 3.25e+01 1cqwA 295 -26.41 -4.43 3.27e+01 1bxm 99 -22.78 -4.42 3.29e+01 1lriA 98 -22.77 -4.41 3.31e+01 1bn6A 294 -26.42 -4.41 3.33e+01 1ezvD 245 -33.69 -4.38 3.41e+01 1cv2A 296 -25.80 -4.38 3.42e+01 2occD 147 -27.77 -4.38 3.43e+01 1eza 259 -27.39 -4.36 3.47e+01 1kf6D 119 -30.48 -4.35 3.52e+01 1h54B 754 -32.99 -4.31 3.64e+01 1bn7A 294 -26.40 -4.31 3.66e+01 1ocrD 147 -27.66 -4.29 3.72e+01 1ekrA 161 -25.61 -4.29 3.73e+01 1f3iA 481 -28.27 -4.27 3.78e+01 3vtk 343 -28.22 -4.26 3.84e+01 1fa0B 537 -28.07 -4.24 3.91e+01 1kutA 230 -25.39 -4.22 3.99e+01 1a0cA 438 -29.05 -4.21 4.00e+01 1gs5A 258 -26.40 -4.21 4.00e+01