% 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.YGR230W.t2k-100-30-stride-ebghtl Host: cc76 Tue Nov 12 18:23:32 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR230W % --------------------------------------------------------------------- % 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 YGR230W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR230W.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 138 nodes, 94.40 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(=1.9059) * Reverse)^tau(=0.7829))) % 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 1ihuA 589 -35.16 -9.86 3.54e-01 1f48A 589 -34.65 -9.46 4.83e-01 1dszA 86 -26.48 -8.50 1.05e+00 1hyqA 263 -28.90 -8.06 1.50e+00 1bza 262 -28.50 -7.81 1.85e+00 1nzyA 269 -29.19 -7.27 2.90e+00 1gnwA 211 -28.98 -7.24 2.98e+00 1gw5B 591 -35.97 -7.05 3.49e+00 1hmcA 148 -29.03 -6.98 3.72e+00 1gdtA 183 -28.15 -6.88 4.05e+00 1a5t 334 -29.06 -6.68 4.78e+00 1g5pA 289 -27.35 -6.56 5.31e+00 1pkn 530 -29.38 -6.54 5.40e+00 1a49A 530 -29.29 -6.38 6.22e+00 1fyeA 229 -26.76 -6.25 6.95e+00 1fy2A 229 -26.76 -6.25 6.96e+00 1hmcB 148 -27.04 -6.22 7.16e+00 1bsg 266 -27.59 -5.98 8.85e+00 1fp6A 289 -27.04 -5.95 9.06e+00 1kwmA 402 -27.33 -5.95 9.08e+00 1k8kE 178 -27.05 -5.92 9.29e+00 1volA 204 -28.35 -5.84 1.00e+01 1h5qA 265 -27.21 -5.79 1.04e+01 1k92A 455 -28.40 -5.76 1.07e+01 1hx0A 496 -27.79 -5.73 1.10e+01 1hra 81 -24.89 -5.70 1.13e+01 1lct 333 -28.00 -5.67 1.15e+01 1a32 88 -26.27 -5.56 1.27e+01 1binA 143 -26.68 -5.54 1.31e+01 1iieA 75 -24.97 -5.52 1.32e+01 1qk8A 146 -24.50 -5.47 1.38e+01 1ep3A 311 -28.82 -5.43 1.44e+01 2ay1A 394 -28.63 -5.40 1.48e+01 1eia 207 -27.83 -5.38 1.50e+01 1hstA 90 -25.54 -5.36 1.53e+01 1fslA 143 -26.40 -5.35 1.54e+01 1tafB 70 -25.08 -5.33 1.57e+01 1ehyA 294 -27.73 -5.27 1.67e+01 1vpt 348 -28.90 -5.21 1.75e+01 1nipA 289 -26.04 -5.20 1.76e+01 1j5vA 351 -26.45 -5.20 1.76e+01 2eiaB 206 -28.03 -5.20 1.77e+01 1vid 221 -26.22 -5.15 1.85e+01 2fsp 124 -25.19 -5.15 1.85e+01 1jsmB 176 -28.60 -5.14 1.87e+01 1k3eA 156 -25.25 -5.10 1.94e+01 1a8y 367 -28.21 -5.09 1.96e+01 1g4wR 383 -27.75 -5.08 1.97e+01 1hr6A 475 -31.73 -5.06 2.00e+01 2aaa 484 -26.74 -5.00 2.12e+01 1jli 112 -26.61 -4.99 2.13e+01 1lxtA 561 -29.01 -4.91 2.30e+01 1g6zA 70 -21.67 -4.88 2.36e+01 3pmgA 561 -29.02 -4.87 2.39e+01 1ekjA 221 -26.86 -4.87 2.39e+01 1ekjB 221 -26.98 -4.86 2.40e+01 4tmkA 213 -27.53 -4.85 2.42e+01 1qgeE 97 -23.24 -4.84 2.46e+01 1bn7A 294 -25.74 -4.83 2.47e+01 1fbaA 361 -26.70 -4.83 2.47e+01 1bob 320 -26.71 -4.81 2.52e+01 2bc2A 227 -24.66 -4.81 2.53e+01 2bc2B 227 -24.66 -4.79 2.57e+01 1cd0A 111 -21.44 -4.74 2.68e+01 1hzoA 271 -25.57 -4.72 2.73e+01 2rslA 140 -25.07 -4.71 2.77e+01 1opp 38 -21.28 -4.71 2.78e+01 1f24A 402 -28.66 -4.69 2.82e+01 1ddcA 247 -26.65 -4.68 2.85e+01 1bu8A 452 -26.48 -4.67 2.86e+01 1jfbA 404 -28.67 -4.66 2.90e+01 5tmpA 213 -27.33 -4.66 2.91e+01 2minA 491 -28.68 -4.62 2.99e+01 1ewxA 146 -23.91 -4.62 3.01e+01 1fpqA 372 -28.63 -4.61 3.04e+01 1c5kA 439 -24.93 -4.60 3.05e+01 1crzA 403 -24.61 -4.58 3.11e+01 1htwA 158 -23.85 -4.57 3.16e+01 1g5cA 170 -25.78 -4.56 3.19e+01 1bn6A 294 -25.70 -4.52 3.29e+01 1dxrL 273 -27.52 -4.51 3.32e+01 6prcL 273 -27.52 -4.50 3.35e+01 1pmi 440 -28.68 -4.43 3.59e+01 1ez1A 392 -25.45 -4.41 3.64e+01 1db3A 372 -26.65 -4.41 3.66e+01 1gjsA 65 -24.03 -4.40 3.68e+01 1e8nA 710 -26.89 -4.39 3.73e+01 1eyzA 392 -25.33 -4.37 3.80e+01 1qfmA 710 -26.89 -4.37 3.81e+01 3minC 491 -28.60 -4.35 3.85e+01 1ash 150 -26.93 -4.34 3.91e+01 1qpcA 279 -27.12 -4.34 3.91e+01 1dl2A 511 -27.85 -4.33 3.95e+01 1thfD 253 -26.12 -4.33 3.95e+01 2lfb 100 -24.52 -4.32 3.98e+01