% 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.T0248.t04-100-30-dssp-ehl2 Host: caw Thu Jul 22 11:52:13 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/casp6/T0248 % --------------------------------------------------------------------- % 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 T0248.t04.w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File T0248.t04.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 6616 sequences, 1561821 residues, 295 nodes, 64.38 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 (=10050) sequences: % N / (1 + exp(-(lambda(=1.7321) * Reverse)^tau(=0.7028))) % 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 1f5qB 252 -30.08 -13.81 9.07e-01 1o86A 589 -29.49 -12.92 1.39e+00 1top 162 -28.51 -12.28 1.90e+00 1mhyB 395 -32.86 -10.87 3.85e+00 1p4xA 250 -25.79 -9.86 6.47e+00 1qsaA 618 -27.59 -9.76 6.83e+00 1ngvA 534 -25.92 -9.71 7.01e+00 1lnwA 147 -23.86 -9.28 8.79e+00 1xwl 580 -28.32 -9.22 9.05e+00 1vk3A 615 -20.65 -9.17 9.30e+00 1g8qA 90 -24.03 -8.96 1.04e+01 1lis 136 -23.34 -8.96 1.04e+01 2lisA 136 -23.34 -8.96 1.04e+01 1nk4A 580 -27.95 -8.94 1.06e+01 1o98A 511 -21.72 -8.82 1.12e+01 1eqjA 511 -21.73 -8.81 1.13e+01 1sly 618 -26.57 -8.79 1.14e+01 1tlqA 189 -26.02 -8.76 1.16e+01 1dxrL 273 -23.58 -8.49 1.35e+01 2occA 514 -23.47 -8.46 1.37e+01 1rtwA 220 -38.01 -8.45 1.37e+01 1b8aA 438 -22.27 -8.43 1.39e+01 1ffyA 917 -27.93 -8.41 1.41e+01 1q0gA 117 -23.96 -8.38 1.43e+01 1lshA 1056 -24.12 -8.36 1.45e+01 1be3G 81 -20.98 -8.32 1.48e+01 1l3sA 580 -27.21 -8.31 1.48e+01 1gnwA 211 -21.36 -8.21 1.57e+01 1ssqA 267 -26.09 -8.18 1.60e+01 1llp 343 -21.00 -8.02 1.74e+01 1j54A 186 -18.28 -7.87 1.89e+01 1obbA 480 -23.80 -7.84 1.92e+01 1rwyA 109 -20.51 -7.83 1.94e+01 1v54A 514 -23.68 -7.81 1.96e+01 1dhn 121 -20.52 -7.63 2.16e+01 1om2A 95 -23.23 -7.63 2.17e+01 1dvkA 173 -24.65 -7.59 2.21e+01 1fx8A 281 -25.31 -7.50 2.34e+01 1v61A 132 -16.72 -7.42 2.44e+01 1m6yA 301 -20.63 -7.40 2.46e+01 1ldfA 281 -26.12 -7.32 2.59e+01 2pgd 482 -26.67 -7.25 2.69e+01 1s0pA 176 -29.75 -7.23 2.72e+01 1i50B 1224 -20.92 -7.22 2.74e+01 1h6pA 203 -26.38 -7.22 2.74e+01 1v9dA 340 -30.32 -7.04 3.03e+01 1l0lG 81 -20.10 -7.04 3.04e+01 1dceA 567 -24.06 -7.02 3.08e+01 1vjqA 79 -16.81 -7.01 3.08e+01 1allA 160 -22.15 -7.01 3.09e+01 1fm2A 169 -21.74 -6.94 3.21e+01 1sur 215 -19.17 -6.94 3.22e+01 1bg6 359 -19.22 -6.90 3.30e+01 1ca1 370 -22.76 -6.81 3.46e+01 1kafA 108 -16.63 -6.76 3.58e+01 1h2sA 225 -23.71 -6.71 3.67e+01 1ls1A 295 -21.45 -6.71 3.68e+01 1nlqA 108 -15.23 -6.63 3.85e+01