% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 02/04/04_14:53:24 % (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. % --------------------------------------------------------------------- % stridefoo.1.YGR217W.t2k-100-30-stride-ebghtl Host: cc85 Thu Feb 26 19:51:32 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR217W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.2ds % % 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 YGR217W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR217W.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 9381 sequences, 2218509 residues, 2040 nodes, 3349.21 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(=1.1951) * Reverse)^tau(=0.7640))) % 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 1top 162 -51.87 -28.41 3.11e-03 1ncx 162 -51.63 -28.36 3.18e-03 1ggzA 148 -49.68 -24.58 1.47e-02 1g4yR 148 -44.32 -24.53 1.50e-02 1j95A 125 -40.97 -23.60 2.20e-02 1iwgA 1053 -67.55 -23.56 2.23e-02 1jvmA 125 -40.24 -23.06 2.75e-02 1zac 90 -40.09 -23.02 2.80e-02 1k4cC 124 -40.76 -22.83 3.03e-02 1r3jC 124 -40.76 -22.83 3.03e-02 1oyeA 1049 -66.52 -22.47 3.51e-02 1cll 148 -48.29 -22.20 3.94e-02 3cln 148 -44.88 -21.31 5.75e-02 1avsA 90 -36.50 -20.93 6.75e-02 1bl8A 97 -37.25 -20.88 6.91e-02 1exrA 148 -47.43 -20.26 8.99e-02 1ehkA 562 -72.70 -19.54 1.23e-01 1osa 148 -46.93 -18.38 2.04e-01 1t1dA 100 -31.63 -18.24 2.17e-01 1jb0A 755 -56.95 -18.17 2.23e-01 1j7rA 86 -32.56 -18.14 2.27e-01 1m46A 148 -33.26 -17.69 2.76e-01 1byyA 53 -29.19 -17.08 3.64e-01 1wdcC 156 -31.85 -16.01 5.91e-01 2mysB 166 -34.97 -15.70 6.78e-01 1ezfA 340 -41.22 -15.11 8.89e-01 1ezvC 385 -56.25 -14.75 1.05e+00 1kb9C 385 -56.25 -14.75 1.05e+00 1a68 95 -26.73 -14.65 1.10e+00 1ho2A 20 -25.88 -14.55 1.15e+00 1kyoC 385 -55.68 -14.50 1.18e+00 1m45A 148 -28.70 -14.22 1.35e+00 1o1fC 147 -30.35 -13.30 2.08e+00 1dsxA 87 -24.87 -12.98 2.42e+00 1bf2 750 -47.00 -12.84 2.58e+00 1qg9A 21 -24.65 -12.55 2.98e+00 9wgaA 171 -38.44 -12.48 3.08e+00 1gweA 503 -41.78 -11.96 3.95e+00 1hbzA 498 -41.09 -11.29 5.51e+00 1p7gA 222 -34.08 -11.26 5.59e+00 2scpA 174 -28.33 -11.25 5.62e+00 1jbaA 204 -28.46 -11.25 5.62e+00 1ggwA 140 -28.41 -11.16 5.86e+00 1wgtA 186 -38.88 -11.07 6.13e+00 1wdcB 156 -28.42 -10.92 6.61e+00 1k94A 165 -32.55 -10.61 7.71e+00 1mhyB 395 -42.20 -10.54 7.98e+00 6prcL 273 -37.06 -10.53 8.02e+00 1f4qA 165 -29.97 -10.50 8.13e+00 1dcnA 424 -30.37 -10.40 8.55e+00 1f5aA 513 -33.63 -10.38 8.66e+00 1q9bA 43 -25.07 -10.29 9.06e+00 1gp0A 143 -23.24 -10.21 9.45e+00 1kplA 473 -45.82 -10.15 9.71e+00 1dceA 567 -39.54 -10.14 9.76e+00 1orsC 132 -40.94 -10.13 9.84e+00 1hev 43 -24.58 -10.03 1.03e+01 1e6fA 143 -22.80 -10.01 1.05e+01 1aijL 281 -39.35 -9.99 1.05e+01 1sva1 361 -35.96 -9.93 1.09e+01 1fchA 368 -32.73 -9.79 1.16e+01 1dxrL 273 -36.19 -9.77 1.18e+01 1nn7A 105 -23.92 -9.71 1.22e+01 1ml9A 302 -32.96 -9.49 1.36e+01 1dcnD 436 -30.12 -9.46 1.38e+01 1qwnA 1045 -40.41 -9.39 1.43e+01 3erk 364 -28.08 -9.37 1.45e+01 1ulkA 126 -32.38 -9.26 1.53e+01 1otsA 465 -44.98 -9.24 1.55e+01 1be3C 379 -45.15 -9.10 1.67e+01 1scmB 145 -25.84 -9.07 1.69e+01 1dhx 967 -57.22 -9.06 1.70e+01 1ctdA 36 -21.33 -9.03 1.73e+01 1n93X 375 -27.29 -9.02 1.74e+01 1fokA 568 -41.78 -8.95 1.80e+01 1nr6A 473 -38.23 -8.84 1.91e+01 1ponA 36 -20.87 -8.84 1.91e+01 1auwA 468 -30.43 -8.81 1.94e+01 1kfuS 184 -32.62 -8.78 1.96e+01 1g8iA 190 -27.91 -8.78 1.97e+01 1ctaA 36 -20.69 -8.76 1.98e+01 1k9uA 78 -25.40 -8.75 1.99e+01 1mwvA 714 -43.34 -8.75 2.00e+01 1phnA 162 -24.81 -8.69 2.06e+01 1js8A 394 -29.28 -8.61 2.15e+01 1r9cA 139 -21.61 -8.57 2.20e+01 1e2uA 553 -41.45 -8.51 2.26e+01 1e1dA 553 -40.99 -8.48 2.30e+01 1br1B 150 -27.16 -8.48 2.30e+01 1po5A 476 -41.61 -8.47 2.32e+01 1gntA 553 -41.32 -8.45 2.33e+01 1ulmA 82 -28.88 -8.31 2.51e+01 1jk0A 419 -34.98 -8.31 2.51e+01 1lk9A 448 -30.25 -8.30 2.53e+01 2btvA 901 -36.07 -8.28 2.56e+01 5pal 109 -22.10 -8.24 2.62e+01 1jf2A 195 -31.26 -8.22 2.64e+01 1lufA 343 -26.90 -8.18 2.70e+01 1dqeA 137 -25.93 -8.18 2.70e+01 1q0sA 259 -29.24 -8.11 2.80e+01 1giqA 413 -34.40 -8.10 2.81e+01 1alvA 173 -30.78 -8.10 2.81e+01 1hcuA 503 -28.03 -8.10 2.81e+01 1pal 108 -21.10 -8.08 2.85e+01 1l6nA 289 -30.92 -8.07 2.86e+01 1n9dA 199 -29.27 -8.01 2.96e+01 1hwwA 1015 -39.35 -8.00 2.98e+01 1i50A 1733 -81.45 -7.97 3.01e+01 1mtyD 512 -37.86 -7.94 3.07e+01 1irxA 523 -39.45 -7.93 3.08e+01 1oohA 126 -23.96 -7.92 3.11e+01 1htyA 1015 -39.19 -7.91 3.12e+01 1hxkA 1015 -39.18 -7.91 3.12e+01 1qcrC 378 -43.62 -7.87 3.18e+01 1egdA 396 -33.88 -7.85 3.22e+01 1fu1B 203 -28.57 -7.84 3.24e+01 1upkA 341 -32.45 -7.77 3.36e+01 1frvB 536 -34.63 -7.77 3.37e+01 1o86A 589 -39.42 -7.76 3.37e+01 1jfkA 134 -24.39 -7.67 3.54e+01 1dugA 234 -30.79 -7.66 3.57e+01 1l7mA 211 -24.59 -7.66 3.57e+01 1fwxA 595 -36.63 -7.64 3.60e+01 1f5sA 211 -24.64 -7.64 3.60e+01 1j97A 211 -24.64 -7.64 3.60e+01 1gupA 348 -28.05 -7.63 3.62e+01 1guqA 348 -27.70 -7.58 3.72e+01 1bi0 226 -22.58 -7.57 3.74e+01 1cb8A 678 -35.17 -7.56 3.75e+01 2dtr 226 -24.70 -7.55 3.79e+01 1m1jA 491 -44.62 -7.51 3.86e+01 1lngA 87 -23.97 -7.49 3.92e+01 1larA 575 -31.02 -7.48 3.93e+01 1qgxA 357 -27.99 -7.48 3.93e+01 1ka1A 357 -27.99 -7.47 3.94e+01 1e12A 253 -33.16 -7.46 3.97e+01