% 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.T0243.t04-100-30-dssp-ebghstl Host: cheep Mon Jul 19 10:58:54 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/casp6/T0243 % --------------------------------------------------------------------- % 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 T0243.t04.w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File T0243.t04.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 6616 sequences, 1561821 residues, 94 nodes, 32.56 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(=1.9418) * Reverse)^tau(=0.7310))) % 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 1cl1A 395 -18.38 -8.84 3.41e+00 1pwaA 162 -15.29 -7.83 6.70e+00 1vk5A 157 -15.64 -7.43 8.80e+00 1f46A 140 -16.07 -7.42 8.89e+00 1c24A 263 -17.52 -7.29 9.71e+00 1hx6A 394 -15.61 -7.07 1.14e+01 1n6zA 105 -15.63 -7.05 1.15e+01 1hssA 124 -15.53 -7.04 1.16e+01 1ig0A 319 -15.74 -7.03 1.17e+01 1ooyA 481 -16.46 -6.77 1.41e+01 1sviA 195 -15.56 -6.63 1.55e+01 1h1dA 221 -16.07 -6.45 1.76e+01 1l0qA 391 -14.42 -6.37 1.87e+01 1kaeA 434 -16.62 -6.33 1.92e+01 1ftrA 296 -14.54 -6.33 1.92e+01 1aba 87 -15.01 -6.13 2.21e+01 1jf8A 131 -15.56 -6.13 2.22e+01 1djxB 624 -14.46 -6.04 2.36e+01 1kqfB 294 -14.14 -6.02 2.40e+01 1vjuA 309 -14.73 -5.99 2.46e+01 1di0A 158 -15.42 -5.98 2.48e+01 1n0wA 243 -14.75 -5.89 2.64e+01 1who 96 -13.63 -5.76 2.91e+01 1t95A 240 -14.36 -5.74 2.96e+01 1tyfA 193 -14.31 -5.70 3.04e+01 1oivA 191 -15.42 -5.59 3.29e+01 1vduA 172 -14.01 -5.59 3.29e+01 1bx4A 345 -14.05 -5.48 3.59e+01 1j26A 112 -15.15 -5.47 3.61e+01 1qhxA 178 -17.24 -5.45 3.66e+01 1v5wA 343 -14.51 -5.42 3.75e+01 1mz4A 137 -13.72 -5.40 3.81e+01 1p9qC 256 -14.40 -5.39 3.83e+01