% 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-dssp-ebghstl Host: cheep Tue Jun 15 22:08:35 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.dssps % % 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.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 6473 sequences, 1530840 residues, 117 nodes, 39.66 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(=1.6962) * Reverse)^tau(=0.7580))) % 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 -45.59 -32.98 6.65e-06 1g7sA 594 -39.45 -26.67 1.54e-04 1f60A 458 -35.20 -22.21 1.58e-03 1exmA 405 -33.66 -19.33 7.55e-03 1ha3A 405 -32.79 -18.63 1.11e-02 1d2eA 397 -29.06 -15.64 6.10e-02 1h8eA 510 -24.34 -12.28 4.54e-01 1e79A 510 -23.92 -12.06 5.22e-01 1d1nA 99 -22.80 -11.56 7.09e-01 1f1gA 154 -20.19 -9.92 2.02e+00 1jcv 153 -19.98 -9.73 2.28e+00 1uvqB 198 -19.85 -9.33 2.98e+00 1ecrA 309 -18.73 -8.33 5.78e+00 1n0uA 842 -21.50 -8.33 5.80e+00 1hdmA 201 -20.49 -7.96 7.47e+00 1ogsA 497 -20.85 -7.95 7.48e+00 1q5hA 147 -21.85 -7.87 7.92e+00 1lw6I 64 -16.41 -7.80 8.32e+00 1aun 208 -17.08 -7.67 9.10e+00 1lvwA 295 -19.40 -7.58 9.66e+00 1dar 691 -21.01 -7.39 1.11e+01 1mp9A 198 -18.24 -7.27 1.20e+01 1b5fB 87 -16.12 -7.20 1.26e+01 1a41 234 -15.71 -6.93 1.53e+01 1tib 269 -16.92 -6.91 1.55e+01 1dq3A 454 -21.62 -6.89 1.57e+01 1ddwA 120 -19.15 -6.73 1.76e+01 1fmtA 314 -16.73 -6.72 1.77e+01 1gt6A 269 -16.51 -6.61 1.92e+01 1bwwA 109 -15.71 -6.59 1.95e+01 1shbA 104 -16.41 -6.58 1.96e+01 1kay 381 -18.78 -6.55 2.00e+01 1am2 199 -20.71 -6.54 2.01e+01 1o4rA 108 -16.34 -6.54 2.02e+01 1bupA 386 -18.76 -6.53 2.03e+01 1shdA 107 -16.81 -6.49 2.08e+01 1k4nA 192 -17.09 -6.44 2.17e+01 1h9dB 134 -17.65 -6.43 2.18e+01 1kxgA 152 -18.35 -6.39 2.25e+01 1hh2P 344 -18.72 -6.23 2.52e+01 1k2eA 156 -18.56 -6.20 2.56e+01 1pk6A 133 -19.22 -6.15 2.67e+01 1ugiA 84 -16.95 -6.12 2.72e+01 1go3E 187 -19.25 -6.10 2.76e+01 1eazA 125 -15.52 -5.95 3.09e+01 1luzA 88 -16.48 -5.94 3.11e+01 1vj1A 363 -16.32 -5.87 3.26e+01 1ly2A 130 -15.57 -5.85 3.32e+01 1ughI 82 -16.42 -5.82 3.39e+01 1h6lA 353 -19.42 -5.77 3.53e+01 1i9zA 347 -18.20 -5.72 3.65e+01 1gppA 237 -19.16 -5.69 3.72e+01 1q2bA 434 -16.43 -5.67 3.79e+01 1is3A 135 -20.12 -5.65 3.84e+01