% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (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-A.t2k-100-30-CB_burial_14_7 Host: farm01 Mon Nov 29 23:49:43 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR027W-A % --------------------------------------------------------------------- % 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 +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR027W-A.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR027W-A.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10944 sequences, 2597075 residues, 441 nodes, 474.00 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 (=10700) sequences: % N / (1 + exp(-(lambda(=1.4619) * Reverse)^tau(=0.7946))) % 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 1mhyG 169 -26.32 -12.46 4.68e-01 1m56B 264 -30.28 -10.74 1.43e+00 1mijA 152 -24.97 -9.98 2.38e+00 1f4qA 165 -23.16 -9.72 2.84e+00 1pu6A 218 -21.24 -9.71 2.86e+00 1har 216 -20.71 -9.31 3.74e+00 1i1rB 181 -19.94 -8.78 5.37e+00 1ra6A 461 -20.14 -8.59 6.10e+00 1bed 181 -20.40 -8.55 6.28e+00 1gdtA 183 -27.44 -8.54 6.33e+00 1gp2G 71 -28.82 -8.43 6.85e+00 1im4A 221 -21.05 -8.40 6.99e+00 1go3F 107 -21.86 -8.10 8.56e+00 1t0hA 132 -21.62 -8.09 8.67e+00 1gw5B 591 -24.23 -7.86 1.01e+01 2end 138 -21.97 -7.85 1.02e+01 1k94A 165 -21.53 -7.83 1.04e+01 1vrtA 560 -20.68 -7.78 1.07e+01 1eduA 149 -20.09 -7.76 1.09e+01 1o26A 232 -22.53 -7.73 1.11e+01 1rthA 560 -20.78 -7.68 1.16e+01 1h67A 108 -21.23 -7.67 1.16e+01 1g8iA 190 -22.21 -7.64 1.19e+01 2hmiA 558 -20.00 -7.62 1.20e+01 1i37A 260 -19.67 -7.54 1.27e+01 1dttA 560 -20.58 -7.38 1.43e+01 1eriA 276 -19.10 -7.35 1.46e+01 1dxrM 323 -22.98 -7.31 1.50e+01 1ckqA 276 -19.07 -7.23 1.59e+01 6prcM 323 -22.44 -7.17 1.66e+01 1h0aA 158 -20.00 -7.13 1.71e+01 1vc1A 110 -17.82 -7.13 1.71e+01 1t7rA 269 -19.47 -7.12 1.72e+01 1f2tB 148 -20.96 -7.10 1.74e+01 1eyhA 144 -19.37 -7.09 1.75e+01 1klo 162 -20.14 -7.08 1.77e+01 1qb2A 109 -22.76 -7.08 1.77e+01 1j1vA 94 -19.06 -7.04 1.81e+01 1x9gA 200 -17.19 -7.01 1.85e+01 1xc2A 263 -26.36 -6.95 1.95e+01 1e08D 88 -32.72 -6.88 2.04e+01 1qtyT 101 -17.39 -6.85 2.09e+01 1on3A 523 -18.42 -6.83 2.12e+01 1ihoA 283 -19.16 -6.79 2.18e+01 1qpsA 261 -18.47 -6.77 2.21e+01 1w0hA 204 -17.82 -6.77 2.21e+01 1o4sA 389 -17.99 -6.75 2.24e+01 1eysH 259 -27.19 -6.74 2.26e+01 1cl8A 276 -18.39 -6.64 2.42e+01 1xfiA 367 -20.00 -6.61 2.49e+01 1fjrA 195 -19.62 -6.55 2.59e+01 1vasA 137 -20.41 -6.53 2.64e+01 1mhyB 395 -22.12 -6.50 2.69e+01 1nz0A 118 -20.78 -6.47 2.75e+01 1r5qA 102 -21.23 -6.46 2.76e+01 1jb7B 260 -26.23 -6.46 2.78e+01 1jhnA 424 -39.01 -6.41 2.88e+01 1jtyA 194 -19.63 -6.38 2.94e+01 1qsvA 101 -16.59 -6.36 2.98e+01 1n1cA 217 -26.51 -6.33 3.06e+01 1ehkB 168 -21.53 -6.31 3.09e+01 1lfdA 87 -17.88 -6.29 3.14e+01 1eemA 241 -19.35 -6.28 3.16e+01 1hfeS 123 -33.09 -6.27 3.18e+01 1aoiD 99 -24.17 -6.24 3.24e+01 1kcmA 270 -20.52 -6.21 3.33e+01 1ddf 127 -21.04 -6.19 3.37e+01 1v74B 87 -18.62 -6.16 3.46e+01 1pvaA 110 -17.67 -6.07 3.68e+01 1foaA 348 -16.67 -6.05 3.73e+01 1blr 137 -18.05 -6.04 3.78e+01 1pt6A 213 -16.83 -6.03 3.79e+01 1fltY 95 -17.28 -6.00 3.88e+01 1bowA 159 -17.50 -6.00 3.89e+01 1fltX 95 -17.28 -5.98 3.95e+01 1ez3A 127 -23.26 -5.98 3.95e+01 1qc9A 276 -17.95 -5.96 4.00e+01