% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 09/03/03_16:30:36 % (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. % --------------------------------------------------------------------- % CB_burial_14_7foo.1.YGR202C.t2k-100-30-CB_burial_14_7 Host: cc46 Sun Oct 12 01:05:29 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR202C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.CB-burial-14-7s % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR202C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR202C.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8763 sequences, 2072585 residues, 425 nodes, 394.46 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 (=8162) sequences: % N / (1 + exp(-(lambda(=1.7253) * Reverse)^tau(=0.7690))) % 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 1cozA 129 -136.35 -111.14 1.52e-21 1mrzA 293 -41.65 -15.29 3.41e-02 1jvr 137 -43.76 -14.76 4.74e-02 1mopA 300 -36.69 -13.91 8.09e-02 1n2eA 300 -36.57 -13.68 9.39e-02 1b6tA 159 -34.44 -11.72 3.37e-01 1ihoA 283 -38.02 -11.51 3.87e-01 1qjcA 158 -33.78 -11.25 4.60e-01 1lrzA 426 -42.75 -10.15 9.70e-01 1od6A 160 -32.29 -9.92 1.13e+00 1lnwA 147 -37.05 -9.45 1.57e+00 1liiA 363 -34.81 -8.83 2.42e+00 1on2A 142 -37.45 -8.01 4.37e+00 1k3yA 221 -32.59 -7.91 4.68e+00 1gseA 221 -32.94 -7.88 4.79e+00 1oxjA 173 -32.73 -7.82 5.01e+00 1k3lA 221 -32.37 -7.76 5.22e+00 1l4sA 112 -34.96 -7.59 5.92e+00 1hx1B 114 -38.22 -7.53 6.19e+00 1g99A 408 -37.68 -7.40 6.79e+00 1jgsA 138 -32.91 -7.09 8.52e+00 1f9aA 168 -31.53 -7.06 8.77e+00 1n3gA 113 -32.27 -6.98 9.28e+00 1dgmA 363 -33.07 -6.96 9.44e+00 1ajqA 209 -38.15 -6.94 9.54e+00 1pkhA 204 -33.48 -6.88 9.97e+00 1ai7A 209 -38.07 -6.84 1.03e+01 1fzvA 132 -35.08 -6.81 1.05e+01 1gm7A 209 -37.32 -6.75 1.10e+01 1e3aA 260 -37.90 -6.74 1.11e+01 1h6pA 203 -30.35 -6.71 1.13e+01 1gm0A 142 -29.96 -6.70 1.14e+01 1j99A 293 -36.83 -6.68 1.16e+01 1j97A 211 -29.28 -6.60 1.23e+01 1f5sA 211 -28.91 -6.55 1.28e+01 1lj9A 144 -33.91 -6.51 1.32e+01 1k4mA 213 -31.40 -6.30 1.55e+01 1pnkA 209 -37.92 -6.29 1.57e+01 1vpfA 102 -34.86 -6.20 1.68e+01 1e0tA 470 -37.54 -6.18 1.69e+01 1gk9A 260 -38.49 -6.14 1.75e+01 1l7mA 211 -28.67 -6.11 1.79e+01 1d4fA 431 -41.44 -6.06 1.86e+01 1bx4A 345 -29.91 -5.99 1.97e+01 1vppV 102 -34.40 -5.99 1.97e+01 1j6uA 469 -32.52 -5.96 2.01e+01 1im5A 180 -27.11 -5.93 2.06e+01 2nllB 103 -32.06 -5.92 2.07e+01 1qfcA 306 -28.55 -5.89 2.12e+01 1mkkA 96 -34.00 -5.84 2.21e+01 1ocyA 198 -43.92 -5.83 2.22e+01 1nogA 177 -28.75 -5.83 2.22e+01 1peh 35 -30.28 -5.76 2.35e+01 1e8cA 498 -35.55 -5.64 2.58e+01 1qh8B 519 -41.51 -5.52 2.83e+01 1qguB 519 -41.51 -5.48 2.93e+01 1b3rA 431 -40.87 -5.47 2.94e+01 1geqA 248 -26.81 -5.45 2.99e+01 1fltV 98 -34.76 -5.45 3.00e+01 1jchA 551 -43.32 -5.39 3.13e+01 1b7fA 168 -29.40 -5.39 3.13e+01 1jchC 551 -43.33 -5.39 3.13e+01 1bs0A 384 -31.87 -5.38 3.16e+01 1iujA 106 -29.55 -5.37 3.19e+01 1h8eG 272 -31.17 -5.33 3.28e+01 1aoa 275 -31.51 -5.31 3.35e+01 1qhhA 167 -35.72 -5.26 3.49e+01 1elvA 333 -36.16 -5.24 3.54e+01 1bhu 102 -24.82 -5.21 3.63e+01 1fs0E 138 -31.51 -5.20 3.65e+01 1c25 161 -27.03 -5.17 3.74e+01 1kyqA 274 -35.55 -5.14 3.84e+01 1f3aA 222 -29.65 -5.12 3.88e+01 1oeyJ 107 -28.67 -5.10 3.95e+01