% 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.YGR027W-B.t2k-100-30-CB_burial_14_7 Host: cc48 Tue Nov 18 02:08:21 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR027W-B % --------------------------------------------------------------------- % 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 YGR027W-B.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR027W-B.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8940 sequences, 2116673 residues, 1756 nodes, 2597.72 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(=1.7922) * Reverse)^tau(=0.7341))) % 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 1asu 162 -94.78 -69.19 9.27e-12 1vsd 152 -88.17 -63.36 7.98e-11 1cxqA 162 -84.64 -60.15 2.67e-10 2itg 163 -74.75 -45.64 7.94e-08 1exqA 154 -64.33 -37.20 2.72e-06 1b9dA 163 -61.96 -36.12 4.35e-06 1hyvA 166 -61.12 -34.28 9.71e-06 1bl3A 160 -59.16 -33.08 1.65e-05 1itg 166 -55.84 -30.15 6.17e-05 1a1tA 55 -48.81 -19.02 1.32e-02 1f6uA 55 -50.81 -18.08 2.15e-02 1mfs 55 -51.44 -18.04 2.20e-02 1aaf 55 -51.19 -17.16 3.47e-02 1nc8 29 -39.69 -15.96 6.59e-02 1dsqA 21 -34.09 -14.83 1.22e-01 1a6bB 40 -45.35 -14.00 1.93e-01 1mml 265 -45.37 -10.02 1.97e+00 1pgtA 210 -36.55 -9.20 3.25e+00 1d1dA 262 -39.02 -9.16 3.33e+00 1hvc 203 -34.97 -8.97 3.76e+00 1f8vA 355 -42.43 -8.87 4.01e+00 1gseA 221 -37.30 -8.10 6.54e+00 1eyhA 144 -33.11 -7.81 7.93e+00 1dwkA 156 -44.66 -7.77 8.13e+00 1dw9A 156 -44.61 -7.77 8.14e+00 1k3lA 221 -36.03 -7.76 8.18e+00 1ltlA 279 -41.71 -7.75 8.24e+00 1miqA 375 -41.22 -7.59 9.16e+00 1qqtA 551 -43.92 -7.56 9.34e+00 1eduA 149 -33.63 -7.53 9.52e+00 1k3yA 221 -35.83 -7.51 9.62e+00 1gm5A 780 -59.84 -7.43 1.01e+01 1h0aA 158 -33.03 -7.35 1.07e+01 1qbqA 333 -42.82 -7.33 1.09e+01 1puoA 170 -31.94 -7.22 1.16e+01 1m2oA 768 -47.21 -7.18 1.20e+01 1f4lA 551 -43.63 -7.09 1.27e+01 1gulA 222 -33.98 -6.93 1.42e+01 1dsvA 31 -32.10 -6.86 1.48e+01 1d9uA 154 -31.12 -6.85 1.49e+01 1dvpA 220 -36.80 -6.79 1.56e+01 1ek9A 428 -51.03 -6.68 1.68e+01 1mhqA 148 -31.66 -6.60 1.77e+01 1cl4A 60 -35.26 -6.59 1.78e+01 1dlc 584 -37.59 -6.55 1.83e+01 1exkA 79 -36.24 -6.55 1.83e+01 1qkkA 155 -31.96 -6.47 1.93e+01 1bolA 222 -31.45 -6.46 1.94e+01 1j8fA 323 -35.12 -6.45 1.97e+01 1mea 28 -28.22 -6.39 2.05e+01 1zin 217 -35.74 -6.37 2.07e+01 1gumA 222 -33.39 -6.34 2.11e+01 1e6bA 221 -33.80 -6.34 2.12e+01 1l6nA 289 -46.05 -6.29 2.19e+01 1o20A 427 -42.57 -6.27 2.22e+01 1omiA 248 -33.01 -6.24 2.27e+01 1o9gA 250 -29.75 -6.09 2.51e+01 1eia 207 -40.69 -6.07 2.55e+01 3egf 53 -30.20 -6.02 2.65e+01 1lylA 504 -43.44 -6.00 2.67e+01 1pdo 135 -29.62 -5.93 2.81e+01 1gqeA 365 -41.34 -5.90 2.87e+01 1gpc 218 -41.26 -5.88 2.90e+01 1g55A 343 -34.90 -5.88 2.90e+01 1gmeA 151 -45.30 -5.82 3.03e+01 1fkmA 396 -36.63 -5.78 3.13e+01 1ku0A 388 -30.83 -5.75 3.18e+01 1qs8A 329 -35.98 -5.74 3.22e+01 1mp9A 198 -34.99 -5.73 3.24e+01 1jplA 171 -32.28 -5.67 3.38e+01 1jb0A 755 -53.13 -5.65 3.41e+01 2eiaB 206 -40.17 -5.60 3.55e+01 1bu5A 147 -28.47 -5.55 3.66e+01 1jp4A 308 -33.85 -5.54 3.70e+01 1e1oA 504 -43.44 -5.54 3.70e+01 1nw3A 416 -39.44 -5.53 3.72e+01 1dk4A 252 -32.66 -5.52 3.75e+01 1g3mA 294 -34.13 -5.52 3.76e+01 1oe8A 211 -33.53 -5.50 3.79e+01 1nf2A 268 -30.47 -5.46 3.91e+01