% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 07/18/04_06:53:46 % (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.T0251.t04-100-30-CB_burial_14_7 Host: ribbit Tue Jul 27 11:46:29 2004 % ggshack Dir: /projects/compbio/experiments/protein-predict/casp6/T0251 % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t04.x-seqs,/projects/compbio/experiments/models.97/indexes/t04.CB-burial-14-7s % % 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 T0251.t04.w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File T0251.t04.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 6648 sequences, 1569757 residues, 103 nodes, 22.38 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 (=10083) sequences: % N / (1 + exp(-(lambda(=1.9154) * Reverse)^tau(=0.7537))) % 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 1grx 85 -20.29 -10.68 6.02e-01 1sly 618 -18.76 -9.91 1.03e+00 1qsaA 618 -18.26 -9.57 1.30e+00 1ql3A 99 -18.99 -9.34 1.53e+00 1t1vA 93 -18.47 -9.03 1.91e+00 1kte 105 -18.34 -8.66 2.50e+00 1j0fA 100 -18.20 -8.57 2.67e+00 1fjgJ 105 -18.50 -8.30 3.24e+00 1h75A 81 -17.73 -7.89 4.39e+00 1ry9A 145 -16.25 -7.10 7.89e+00 1o0pA 104 -16.65 -6.98 8.69e+00 1m2dA 110 -16.60 -6.86 9.48e+00 1q4mA 221 -15.73 -6.77 1.02e+01 1r5pA 108 -16.77 -6.70 1.07e+01 1a8h 500 -17.24 -6.62 1.14e+01 1s1hM 132 -15.62 -6.38 1.38e+01 1ns5A 155 -15.66 -6.33 1.42e+01 1lv3A 68 -16.37 -6.29 1.48e+01 1lm6A 215 -14.76 -6.13 1.67e+01 1j34A 129 -15.08 -6.08 1.74e+01 1gzgA 337 -17.88 -5.88 2.03e+01 1jmxA 494 -14.42 -5.85 2.09e+01 1v65A 64 -18.12 -5.71 2.34e+01 1vjqA 79 -14.97 -5.70 2.35e+01 1s7zA 117 -16.84 -5.42 2.93e+01 1mszA 86 -14.73 -5.42 2.95e+01 1phk 298 -13.94 -5.41 2.96e+01 1tiiC 53 -15.88 -5.38 3.04e+01 2ezk 99 -16.38 -5.32 3.19e+01 1s4nA 348 -14.81 -5.31 3.21e+01 1f37A 110 -15.08 -5.22 3.46e+01 3daaA 277 -13.74 -5.18 3.57e+01 1a8y 367 -15.56 -5.15 3.65e+01 1vsd 152 -13.29 -5.11 3.80e+01 1xgsA 295 -13.11 -5.10 3.81e+01 1a8o 70 -14.00 -5.07 3.92e+01