% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 02/04/04_14:53:24 % (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. % --------------------------------------------------------------------- % dsspfoo.1.T0196.t04-100-30-stride-ebghtl Host: cheep Tue Jun 15 22:07:17 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/casp6/T0196 % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t04.x-seqs,/projects/compbio/experiments/models.97/indexes/t04.2ds % % 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 T0196.t04.w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File T0196.t04.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 6473 sequences, 1530840 residues, 117 nodes, 37.69 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 (=9907) sequences: % N / (1 + exp(-(lambda(=1.5239) * Reverse)^tau(=0.7894))) % 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 1jnyA 435 -47.77 -33.36 2.20e-06 1g7sA 594 -41.31 -27.44 5.27e-05 1f60A 458 -37.20 -22.26 9.58e-04 1exmA 405 -36.46 -20.29 2.99e-03 1ha3A 405 -36.28 -20.23 3.11e-03 1d2eA 397 -32.24 -16.42 3.01e-02 1d1nA 99 -25.29 -14.07 1.30e-01 1e79A 510 -24.08 -10.80 1.08e+00 1h8eA 510 -24.17 -10.73 1.13e+00 1uvqB 198 -21.48 -10.41 1.40e+00 1f1gA 154 -19.73 -8.61 4.80e+00 1jcv 153 -19.52 -8.49 5.25e+00 1eazA 125 -18.85 -7.96 7.62e+00 1dar 691 -22.09 -7.84 8.31e+00 1ddwA 120 -20.38 -7.79 8.56e+00 1lvwA 295 -19.69 -7.70 9.13e+00 1hh2P 344 -19.59 -7.53 1.03e+01 1n0uA 842 -20.46 -7.44 1.10e+01 2hgsA 474 -23.35 -7.40 1.14e+01 1k4nA 192 -18.77 -7.35 1.18e+01 1mp9A 198 -19.22 -7.30 1.22e+01 1kxgA 152 -20.81 -7.19 1.32e+01 1ogsA 497 -19.38 -7.17 1.34e+01 1ecrA 309 -18.26 -7.11 1.40e+01 1go3E 187 -22.95 -7.08 1.43e+01 1ly2A 130 -17.57 -7.06 1.45e+01 1tib 269 -17.93 -6.94 1.59e+01 1r94A 118 -20.81 -6.89 1.65e+01 1k82A 268 -17.64 -6.79 1.77e+01 1hdmA 201 -19.26 -6.73 1.85e+01 1aun 208 -17.20 -6.67 1.93e+01 1gt6A 269 -17.24 -6.66 1.95e+01 1b5fB 87 -15.31 -6.61 2.02e+01 1e3dB 542 -17.06 -6.40 2.35e+01 1fmtA 314 -17.75 -6.35 2.44e+01 1uj2A 252 -16.16 -6.35 2.45e+01 1h2rL 534 -17.24 -6.34 2.48e+01 1ghqB 134 -16.03 -6.23 2.68e+01 1lvmA 229 -18.99 -6.15 2.85e+01 1p32A 209 -19.25 -6.13 2.89e+01 1g8lA 411 -16.56 -6.13 2.90e+01 1pvmA 184 -15.93 -6.06 3.05e+01 1ubkL 534 -17.18 -6.04 3.09e+01 1rovA 857 -17.27 -6.04 3.10e+01 1iwdA 215 -15.75 -5.99 3.21e+01 1j6qA 136 -20.33 -5.97 3.25e+01 1jyhA 157 -16.79 -5.95 3.30e+01 1bwwA 109 -15.14 -5.92 3.39e+01 1njkA 156 -19.13 -5.88 3.47e+01 1ep0A 185 -19.78 -5.86 3.53e+01 1k2eA 156 -20.73 -5.86 3.53e+01 1q5hA 147 -19.22 -5.84 3.60e+01 1ewkA 490 -15.60 -5.82 3.64e+01 1i8dA 213 -17.39 -5.82 3.66e+01 1efvA 315 -16.13 -5.73 3.91e+01