% 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.T0239.t04-100-30-dssp-ebghstl Host: abyss Tue Jul 13 11:51:35 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/casp6/T0239 % --------------------------------------------------------------------- % 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 T0239.t04.w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File T0239.t04.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 6616 sequences, 1561821 residues, 99 nodes, 23.41 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 (=10050) sequences: % N / (1 + exp(-(lambda(=1.7149) * Reverse)^tau(=0.8077))) % 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 1k8kD 300 -17.78 -7.76 3.07e+00 1earA 147 -16.75 -7.54 3.70e+00 1p4xA 250 -17.18 -7.51 3.81e+00 1d8hA 311 -16.10 -7.14 5.21e+00 1mp9A 198 -16.72 -6.98 5.99e+00 1j7xA 302 -15.81 -6.88 6.53e+00 1mk0A 97 -15.14 -6.54 8.75e+00 1g2rA 100 -14.64 -6.47 9.25e+00 1qgvA 142 -15.53 -6.32 1.06e+01 1ly2A 130 -16.31 -6.31 1.07e+01 1psdA 409 -14.62 -6.29 1.09e+01 1ef1A 294 -16.14 -6.28 1.10e+01 1h6kA 757 -16.12 -6.23 1.15e+01 1s6bB 119 -14.54 -6.02 1.37e+01 1mai 131 -14.64 -5.93 1.49e+01 1s6bA 119 -14.01 -5.88 1.56e+01 1lmeA 176 -15.90 -5.82 1.64e+01 1s7oA 113 -14.02 -5.80 1.68e+01 1q6cA 495 -15.08 -5.77 1.72e+01 1lfjA 119 -13.76 -5.73 1.79e+01 1iujA 106 -15.61 -5.72 1.80e+01 1byb 495 -15.06 -5.72 1.80e+01 1poa 118 -14.28 -5.69 1.85e+01 1o86A 589 -14.97 -5.69 1.86e+01 1ghqB 134 -15.27 -5.57 2.06e+01 1q0bA 367 -15.35 -5.54 2.12e+01 1fiuA 286 -13.67 -5.48 2.22e+01 1vk8A 106 -14.49 -5.33 2.56e+01 1ab8A 220 -15.89 -5.16 2.98e+01 1h9oA 112 -13.99 -5.14 3.02e+01 1c0pA 363 -15.11 -5.12 3.08e+01 1b7yB 785 -14.45 -5.09 3.17e+01 1aqzA 149 -13.88 -5.07 3.23e+01 1ry6A 360 -14.29 -5.04 3.32e+01 1aisA 182 -14.56 -5.04 3.33e+01 1o8vA 134 -13.94 -4.96 3.58e+01 1oe0A 230 -13.62 -4.93 3.67e+01 1jb0D 138 -12.76 -4.91 3.75e+01 1c2aA 120 -16.34 -4.90 3.78e+01 1svsA 353 -13.94 -4.86 3.91e+01 1r0wA 286 -13.65 -4.86 3.93e+01