% SAM: /projects/compbio/bin/i686/hmmscore v3.3.2 (February, 2001) compiled 06/24/02_10:50:12 % (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-T99, 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, C. Barrett, R. Hughey, Hidden Markov models for detecting % remote protein homologies, Bioinformatics 14(10):846-856, 1998. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % w0.5foo.1.YEL028W.t2k-w0.5.mod Host: cc74 Sat Nov 2 12:00:51 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YEL0/YEL028W % --------------------------------------------------------------------- % Inserted Files: YEL028W.t2k-w0.5.mod % Database Files: /projects/compbio/experiments/protein-predict/SAM_T02/data/pdbaa % % 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)) % Single Track Model: YEL028W.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13975 sequences, 3107935 residues, 154 nodes, 152.22 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 (=7316) sequences: % N / (1 + exp(-(lambda(=2.7924) * Reverse)^tau(=0.7242))) % 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 1l7iH 222 -29.44 -10.16 9.26e-02 1erjA 393 -29.25 -7.70 7.23e-01 1ad0B 220 -26.99 -7.60 7.86e-01 1qfwH 117 -24.69 -7.00 1.34e+00 1cloH 222 -25.68 -6.26 2.60e+00 1qo7A 394 -26.90 -5.97 3.40e+00 1a0i 348 -26.37 -5.88 3.69e+00 1d6tA 117 -23.78 -5.85 3.82e+00 1hizA 379 -26.80 -5.76 4.12e+00 1eyxA 164 -24.20 -5.66 4.54e+00 1gp1A 198 -24.98 -5.36 6.02e+00 1lr6A 82 -22.38 -5.32 6.30e+00 1d9kB 112 -22.92 -5.27 6.60e+00 1mimH 215 -24.80 -5.25 6.71e+00 1jtoA 148 -24.00 -4.97 8.86e+00 1i5sA 367 -25.65 -4.87 9.77e+00 1i6iA 366 -25.61 -4.83 1.01e+01 1ia0K 394 -25.69 -4.76 1.09e+01 1lnrX 55 -20.94 -4.75 1.10e+01 1e0oD 219 -24.31 -4.69 1.17e+01 1ev2E 220 -24.32 -4.68 1.17e+01 1ii4E 220 -24.29 -4.68 1.17e+01 1iilG 220 -24.31 -4.68 1.18e+01 1djsA 216 -24.30 -4.65 1.21e+01 1gw0A 559 -26.65 -4.65 1.21e+01 2napA 723 -27.12 -4.65 1.22e+01 1b8dA 164 -23.12 -4.59 1.28e+01 1b0uA 262 -24.17 -4.50 1.41e+01 1d6vH 221 -25.54 -4.46 1.46e+01 1js3A 486 -25.41 -4.46 1.47e+01 2hrpH 226 -24.29 -4.43 1.51e+01 2tunA 157 -23.44 -4.38 1.59e+01 1lcjA 109 -22.44 -4.36 1.61e+01 1bhfA 108 -22.41 -4.35 1.63e+01 1bwmA 249 -23.73 -4.34 1.65e+01 2fb4H 229 -23.90 -4.32 1.69e+01 1lkkA 105 -22.21 -4.25 1.81e+01 1jtrB 237 -23.88 -4.25 1.82e+01 1jtpA 148 -23.27 -4.24 1.83e+01 1lklA 104 -22.15 -4.23 1.85e+01 1bhhB 103 -22.12 -4.23 1.85e+01 1axsB 221 -25.37 -4.22 1.86e+01 1d5bB 221 -25.37 -4.22 1.86e+01 1nobA 185 -23.24 -4.21 1.89e+01 1cwdL 98 -21.95 -4.20 1.91e+01 1lc5A 364 -25.22 -4.19 1.92e+01 1lkcA 364 -25.22 -4.19 1.92e+01 1m20A 82 -21.20 -4.18 1.95e+01 1eah1 301 -24.50 -4.17 1.96e+01 1a7i 81 -21.58 -4.13 2.04e+01 1ijrA 104 -22.11 -4.12 2.08e+01 1mcpH 222 -23.50 -4.10 2.12e+01 1ehlH 219 -23.89 -4.09 2.13e+01 1kg0C 136 -23.86 -4.08 2.17e+01 1liaA 164 -22.83 -4.07 2.17e+01 1fbzA 104 -22.08 -4.07 2.17e+01 1jttA 133 -22.76 -4.07 2.19e+01 1ehbA 82 -21.00 -3.98 2.40e+01 1kv8A 216 -23.28 -3.96 2.44e+01 1ib7A 94 -21.54 -3.96 2.44e+01 1iow 306 -24.48 -3.93 2.53e+01 1bxnA 485 -25.40 -3.91 2.57e+01 2igfH 221 -23.67 -3.91 2.58e+01 1cdwA 179 -22.84 -3.88 2.66e+01 1h8lA 380 -27.64 -3.82 2.83e+01 1qmuA 380 -27.64 -3.82 2.83e+01 1fgvH 124 -22.39 -3.82 2.83e+01 1lqxA 82 -20.85 -3.80 2.89e+01 7pcy 98 -21.26 -3.79 2.91e+01 2axx 94 -21.36 -3.78 2.95e+01 1aw3 94 -21.36 -3.77 2.96e+01 1lmkA 238 -24.72 -3.76 3.01e+01 1i87A 98 -21.41 -3.76 3.01e+01 2dln 306 -24.48 -3.76 3.02e+01 1bfx 99 -21.42 -3.75 3.03e+01 1do9A 94 -21.17 -3.74 3.06e+01 1c9bB 180 -22.65 -3.71 3.17e+01 1qnzH 119 -21.78 -3.70 3.21e+01 2ig2H 455 -24.59 -3.68 3.27e+01 1jfiC 185 -22.68 -3.67 3.30e+01 1tghA 185 -22.68 -3.67 3.30e+01 1cyo 93 -21.20 -3.65 3.37e+01 1vokA 200 -22.63 -3.65 3.39e+01 1qnaA 200 -22.63 -3.65 3.39e+01 1avoB 140 -21.73 -3.63 3.46e+01 4tsvA 150 -22.55 -3.61 3.53e+01 1jexA 94 -20.95 -3.59 3.61e+01 1f11B 221 -23.33 -3.54 3.81e+01 1a8mA 157 -22.65 -3.53 3.83e+01 1l0yA 236 -23.11 -3.51 3.94e+01 1bec 238 -23.12 -3.50 3.99e+01