% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (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-T2K, 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, et al., What is the value added by human intervention in protein % structure prediction, Proteins: Stucture, Function, Genetics 45(S5):86--91, 2001. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % stridefoo.1.YGR027W-A.t2k-100-30-stride-ebghtl Host: farm01 Mon Nov 29 23:18:10 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR027W-A % --------------------------------------------------------------------- % 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 +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR027W-A.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR027W-A.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10944 sequences, 2597075 residues, 441 nodes, 468.21 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 (=10700) sequences: % N / (1 + exp(-(lambda(=1.2600) * Reverse)^tau(=0.7883))) % 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 1fonA 240 -24.60 -12.48 1.66e+00 1n45A 233 -25.16 -12.25 1.87e+00 1o4sA 389 -23.90 -12.01 2.15e+00 1qkkA 155 -21.35 -11.74 2.50e+00 1ois 223 -24.85 -11.49 2.87e+00 1l5zA 155 -21.27 -11.45 2.94e+00 1kf6A 602 -23.94 -11.19 3.40e+00 1hlvA 131 -23.21 -11.04 3.71e+00 1rtwA 220 -28.06 -11.04 3.72e+00 1iq3A 110 -24.30 -10.97 3.87e+00 1lwdA 413 -22.72 -10.76 4.35e+00 1peqA 714 -21.35 -10.71 4.46e+00 1h3fA 432 -21.28 -10.60 4.77e+00 1w7bA 339 -25.93 -10.59 4.78e+00 1klt 226 -23.61 -10.28 5.73e+00 1oshA 232 -24.32 -10.27 5.76e+00 1pv6A 417 -29.77 -10.14 6.22e+00 1ljrA 244 -22.00 -10.13 6.24e+00 1hizA 379 -24.06 -9.67 8.18e+00 1lwyA 324 -22.28 -9.44 9.34e+00 1f7cA 231 -24.11 -9.30 1.02e+01 1qusA 322 -21.78 -9.26 1.04e+01 1ltm 320 -21.82 -9.21 1.07e+01 1lnrI 134 -23.42 -9.11 1.14e+01 1guxB 152 -21.05 -8.96 1.24e+01 1ko9A 345 -22.65 -8.94 1.26e+01 1eemA 241 -21.72 -8.94 1.26e+01 1cqxA 403 -23.18 -8.93 1.26e+01 1qmhA 347 -20.48 -8.85 1.32e+01 1nn6A 228 -21.67 -8.81 1.35e+01 1kxpD 458 -24.51 -8.79 1.37e+01 1paqA 189 -26.57 -8.78 1.38e+01 1dk8A 147 -23.31 -8.66 1.49e+01 1m1cA 680 -23.47 -8.63 1.51e+01 1g5yA 238 -21.67 -8.63 1.51e+01 1hw1A 239 -23.43 -8.63 1.52e+01 1fftC 204 -25.50 -8.61 1.53e+01 1go3F 107 -22.55 -8.56 1.57e+01 1eh2 106 -21.66 -8.52 1.62e+01 1cpt 412 -21.53 -8.32 1.81e+01 1mhyG 169 -21.61 -8.26 1.89e+01 1fqvJ 149 -20.71 -8.24 1.91e+01 1siqA 392 -22.17 -8.22 1.93e+01 1s9pA 227 -21.85 -8.21 1.94e+01 1pjpA 226 -21.69 -8.21 1.94e+01 1k30A 368 -19.94 -8.13 2.04e+01 1k8eA 345 -21.35 -8.10 2.08e+01 1o17A 345 -21.35 -8.10 2.08e+01 1fqvD 149 -20.60 -8.08 2.11e+01 1jk0B 345 -23.60 -8.04 2.16e+01 1iuqA 367 -19.77 -8.01 2.20e+01 1sr7A 259 -21.22 -7.99 2.22e+01 1cipA 353 -21.48 -7.92 2.32e+01 1mroA 548 -19.00 -7.86 2.40e+01 1hbnA 549 -18.98 -7.86 2.40e+01 1om2A 95 -20.35 -7.84 2.43e+01 1iqrA 420 -21.07 -7.78 2.53e+01 1e79D 482 -19.35 -7.78 2.53e+01 1tu3F 79 -20.09 -7.70 2.66e+01 7catA 506 -24.76 -7.69 2.67e+01 1gkgA 136 -19.49 -7.64 2.75e+01 1r5qA 102 -24.66 -7.63 2.77e+01 1bed 181 -20.93 -7.63 2.77e+01 1pu6A 218 -22.36 -7.62 2.79e+01 1gxuA 91 -16.71 -7.61 2.79e+01 1t07A 94 -18.66 -7.61 2.80e+01 1qq8A 214 -20.58 -7.59 2.84e+01 1iow 306 -18.03 -7.56 2.89e+01 1n83A 270 -25.75 -7.49 3.02e+01 1u11A 182 -20.37 -7.47 3.06e+01 1pt7A 437 -19.11 -7.45 3.08e+01 2dln 306 -17.74 -7.45 3.10e+01 1q7eA 428 -19.16 -7.38 3.22e+01 1u08A 386 -17.97 -7.38 3.23e+01 1h67A 108 -19.48 -7.35 3.28e+01 1j4nA 271 -21.61 -7.34 3.31e+01 1wmuA 141 -21.22 -7.32 3.35e+01 1w53A 84 -19.29 -7.32 3.36e+01 1huw 166 -21.44 -7.28 3.43e+01 1j78A 458 -24.02 -7.27 3.46e+01 1oe8A 211 -22.03 -7.25 3.50e+01 1hh8A 213 -19.99 -7.24 3.53e+01 1sqnA 261 -21.12 -7.23 3.55e+01 1a28A 256 -21.08 -7.23 3.55e+01 1eceA 358 -20.14 -7.22 3.56e+01 1qcrA 446 -20.52 -7.22 3.58e+01 1v74B 87 -19.37 -7.21 3.59e+01 1myt 146 -21.87 -7.18 3.66e+01 1bg4 302 -20.27 -7.16 3.70e+01 1mlwA 301 -21.11 -7.12 3.79e+01 1b31A 302 -20.27 -7.11 3.83e+01 1nxcA 478 -19.93 -7.10 3.84e+01 1w0hA 204 -19.39 -7.09 3.86e+01 1d0bA 213 -19.07 -7.09 3.86e+01 1izcA 339 -18.56 -7.09 3.86e+01 1el6B 219 -17.82 -7.07 3.92e+01 1hx1B 114 -25.36 -7.06 3.93e+01 1uxtA 501 -19.25 -7.06 3.95e+01