% 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. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YGR027W-A.t2k-100-30-dssp-ehl2 Host: farm01 Mon Nov 29 23:33:54 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.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 YGR027W-A.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR027W-A.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10944 sequences, 2597075 residues, 441 nodes, 465.94 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(=1.5375) * Reverse)^tau(=0.7427))) % 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 1fftC 204 -28.45 -13.86 6.56e-01 1o4sA 389 -24.01 -12.77 1.17e+00 1qkkA 155 -22.22 -12.56 1.30e+00 1l5zA 155 -22.19 -12.46 1.37e+00 1fonA 240 -24.72 -11.40 2.43e+00 1peqA 714 -22.22 -11.26 2.62e+00 1iq3A 110 -22.61 -10.31 4.46e+00 1w0hA 204 -21.31 -9.91 5.58e+00 1pu6A 218 -22.90 -9.64 6.49e+00 1t7rA 269 -23.02 -9.58 6.73e+00 1hlvA 131 -20.79 -9.51 6.99e+00 1v74B 87 -20.99 -9.46 7.21e+00 1qusA 322 -21.09 -9.37 7.59e+00 1i37A 260 -22.66 -9.31 7.85e+00 1paqA 189 -25.64 -9.20 8.38e+00 1ltm 320 -20.95 -9.11 8.80e+00 1lwdA 413 -20.86 -8.88 1.01e+01 1kf6A 602 -20.62 -8.85 1.02e+01 1g8iA 190 -24.79 -8.84 1.03e+01 1eemA 241 -20.97 -8.78 1.07e+01 1iqrA 420 -22.72 -8.77 1.07e+01 1mhyB 395 -26.50 -8.66 1.14e+01 1w7bA 339 -23.45 -8.66 1.15e+01 1f7cA 231 -21.73 -8.59 1.19e+01 1qmhA 347 -19.87 -8.51 1.25e+01 1sr7A 259 -20.89 -8.44 1.31e+01 1m1cA 680 -21.48 -8.38 1.35e+01 1n45A 233 -20.71 -8.32 1.40e+01 1a28A 256 -20.90 -8.29 1.42e+01 1sqnA 261 -20.97 -8.22 1.49e+01 1k8eA 345 -20.19 -8.16 1.54e+01 1o17A 345 -20.19 -8.16 1.54e+01 1tqgA 105 -22.86 -8.13 1.56e+01 1cqxA 403 -21.32 -8.11 1.59e+01 1gkgA 136 -20.74 -8.08 1.61e+01 1ib2A 349 -21.53 -7.96 1.74e+01 1qq8A 214 -19.96 -7.92 1.78e+01 1w68A 390 -24.25 -7.92 1.78e+01 1h3fA 432 -18.35 -7.88 1.81e+01 1pv6A 417 -25.19 -7.76 1.96e+01 1h67A 108 -20.04 -7.71 2.01e+01 1rtwA 220 -23.59 -7.71 2.02e+01 1pbp 321 -18.10 -7.70 2.03e+01 1aq6A 253 -17.73 -7.68 2.05e+01 1n83A 270 -25.25 -7.64 2.10e+01 1t07A 94 -18.52 -7.56 2.21e+01 1klt 226 -19.57 -7.56 2.21e+01 1oshA 232 -21.01 -7.52 2.25e+01 1kxpD 458 -23.21 -7.51 2.28e+01 1xsm 390 -25.80 -7.50 2.29e+01 1ezvD 245 -23.36 -7.48 2.31e+01 1u08A 386 -17.83 -7.41 2.42e+01 1nn6A 228 -20.13 -7.38 2.46e+01 1h0oA 390 -25.61 -7.32 2.55e+01 1izcA 339 -18.81 -7.26 2.65e+01 1omrA 201 -20.66 -7.25 2.65e+01 1kyoD 248 -22.86 -7.21 2.74e+01 1dk8A 147 -20.84 -7.20 2.75e+01 1uxtA 501 -19.48 -7.19 2.77e+01 1odoA 408 -20.68 -7.16 2.82e+01 1tu3F 79 -18.72 -7.13 2.86e+01 1mhyG 169 -19.90 -7.11 2.89e+01 1qq5A 253 -17.08 -7.11 2.91e+01 1guxB 152 -18.78 -7.10 2.91e+01 1qq7A 253 -17.06 -7.07 2.98e+01 1ivhA 394 -19.05 -7.05 3.00e+01 1bed 181 -19.30 -7.03 3.04e+01 1kb9D 246 -22.76 -7.01 3.08e+01 1ljrA 244 -17.89 -6.97 3.16e+01 1rec 201 -20.39 -6.96 3.19e+01 1pjpA 226 -19.43 -6.94 3.22e+01 1e2xA 243 -21.07 -6.83 3.45e+01 1j78A 458 -22.20 -6.82 3.47e+01 4icb 76 -18.80 -6.82 3.47e+01 1w32A 348 -19.87 -6.82 3.48e+01 1go3F 107 -19.69 -6.80 3.51e+01 1hw1A 239 -20.80 -6.80 3.52e+01 1vp4A 425 -18.99 -6.80 3.53e+01 1pvaA 110 -19.46 -6.79 3.53e+01 1ouvA 273 -18.96 -6.79 3.55e+01 2ki5A 366 -17.44 -6.78 3.55e+01 1skyE 473 -18.15 -6.77 3.58e+01 1e2kA 331 -17.28 -6.76 3.60e+01 1ixh 321 -17.25 -6.75 3.63e+01 1qhiA 366 -17.42 -6.74 3.65e+01 1r85A 379 -21.16 -6.74 3.66e+01 1iqqA 200 -18.61 -6.73 3.66e+01 1hizA 379 -21.13 -6.73 3.66e+01 2tct 207 -20.45 -6.73 3.67e+01 1be3A 446 -19.59 -6.70 3.73e+01 1euhA 475 -17.47 -6.68 3.78e+01 1kimA 366 -17.29 -6.65 3.87e+01 1qoyA 318 -21.54 -6.63 3.92e+01 1bjz 207 -20.19 -6.62 3.92e+01 1eceA 358 -19.94 -6.62 3.93e+01