% 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. % --------------------------------------------------------------------- % strfoo.1.YDL102W.t2k-100-30-str Host: cc76 Mon Nov 11 18:13:18 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YDL1/YDL102W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.strs % % 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 YDL102W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YDL102W.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 1098 nodes, 907.46 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(=1.1852) * Reverse)^tau(=0.7025))) % 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 1tgoA 773 -765.74 -715.42 2.14e-46 1qhtA 775 -706.17 -659.03 1.28e-43 1clqA 903 -493.70 -438.42 5.60e-32 1noyA 388 -207.73 -176.45 2.17e-15 1nozA 388 -201.41 -170.87 5.62e-15 1fxxA 482 -51.46 -22.86 2.85e-01 1j54A 186 -45.08 -20.22 6.59e-01 1k5dB 201 -45.71 -16.97 1.94e+00 1t7pA 698 -64.08 -16.33 2.42e+00 1g60A 260 -41.78 -15.68 3.03e+00 1cf9A 753 -65.21 -15.55 3.16e+00 1bcpB 199 -40.69 -14.19 5.13e+00 1k32A 1045 -84.16 -13.85 5.80e+00 1jepA 222 -40.83 -13.77 5.97e+00 1yprA 125 -38.36 -13.65 6.23e+00 1bcpC 199 -40.01 -13.58 6.38e+00 1eypA 222 -40.61 -13.52 6.52e+00 1k0rA 366 -41.77 -13.32 7.02e+00 1eyqA 222 -40.03 -13.01 7.88e+00 1b35A 260 -38.26 -12.83 8.42e+00 1e8xA 961 -59.97 -12.75 8.69e+00 1evhA 112 -38.27 -12.20 1.06e+01 1ewqA 765 -46.85 -12.01 1.14e+01 1bvqA 141 -36.45 -11.82 1.23e+01 3sxlA 184 -36.19 -11.79 1.24e+01 1kcfA 258 -39.16 -11.67 1.30e+01 1jj2B 337 -48.92 -11.64 1.31e+01 1j78A 458 -42.08 -11.48 1.40e+01 1cknA 330 -46.70 -11.40 1.44e+01 1gm6A 175 -48.65 -11.39 1.45e+01 1htwA 158 -35.53 -11.37 1.46e+01 1bhgA 613 -44.05 -11.36 1.46e+01 1ci3M 249 -40.16 -11.35 1.47e+01 1e7uA 961 -59.99 -11.33 1.48e+01 1edt 271 -37.81 -11.31 1.49e+01 1b8aA 438 -46.01 -11.24 1.53e+01 1d0nA 729 -63.01 -11.11 1.61e+01 1l5cA 92 -33.97 -11.02 1.67e+01 1rthA 560 -49.68 -11.00 1.68e+01 1e8yA 966 -59.18 -10.95 1.71e+01 1vrtA 560 -49.62 -10.93 1.73e+01 1b1cA 181 -35.41 -10.93 1.73e+01 1f8nA 839 -55.90 -10.88 1.77e+01 1em2A 229 -39.94 -10.86 1.78e+01 1l3kA 196 -36.02 -10.82 1.80e+01 1jug 125 -31.78 -10.73 1.86e+01 4rhv3 236 -38.93 -10.66 1.92e+01 1amoA 615 -44.24 -10.55 2.00e+01 1h4vB 421 -39.88 -10.47 2.07e+01 1eejA 216 -34.69 -10.40 2.13e+01 1k8kC 372 -44.65 -10.30 2.21e+01 1b3tA 147 -34.42 -10.27 2.24e+01 1igwA 434 -39.51 -10.26 2.24e+01 2hmiA 558 -48.49 -10.26 2.24e+01 1lo7A 141 -35.46 -10.23 2.27e+01 1e8gA 560 -54.29 -10.23 2.27e+01 1fxlA 167 -33.04 -10.19 2.31e+01 1yge 839 -55.98 -10.17 2.33e+01 1ha1 184 -34.65 -10.11 2.39e+01 1ivwA 638 -59.54 -10.06 2.43e+01 1dq3A 454 -45.91 -10.02 2.47e+01 1lnh 857 -57.89 -9.88 2.61e+01 1b9mA 265 -36.70 -9.88 2.61e+01 1qqyA 130 -30.90 -9.86 2.63e+01 2bopA 85 -30.67 -9.85 2.64e+01 1h9sA 140 -35.13 -9.84 2.66e+01 1exqA 154 -33.82 -9.83 2.66e+01 1aua 296 -35.14 -9.81 2.68e+01 1mml 265 -34.86 -9.76 2.74e+01 1qltA 560 -53.78 -9.73 2.78e+01 1chuA 540 -44.64 -9.73 2.78e+01 1fgqA 839 -54.47 -9.72 2.78e+01 2gsq 202 -36.06 -9.69 2.81e+01 1ihrA 76 -31.86 -9.61 2.91e+01 1kr4A 125 -37.05 -9.59 2.93e+01 1ieaA 192 -38.53 -9.57 2.96e+01 1hd8A 363 -42.82 -9.51 3.03e+01 1k0iA 394 -39.76 -9.48 3.07e+01 1vaoA 560 -52.89 -9.46 3.09e+01 1kxpD 458 -40.17 -9.46 3.09e+01 1eo9A 209 -34.73 -9.44 3.12e+01 1hzgA 295 -40.27 -9.42 3.15e+01 1qguB 519 -39.92 -9.41 3.15e+01 1qfmA 710 -58.51 -9.40 3.16e+01 1nmtA 392 -42.59 -9.40 3.17e+01 1cvjB 190 -33.78 -9.39 3.18e+01 1faoA 126 -34.75 -9.36 3.21e+01 1fl9A 161 -32.83 -9.35 3.23e+01 1ezvF 125 -33.09 -9.29 3.31e+01 1rhi3 236 -37.42 -9.26 3.35e+01 1b7fA 168 -33.68 -9.19 3.45e+01 1sig 339 -37.61 -9.17 3.48e+01 1qh8B 519 -39.67 -9.16 3.49e+01 1e8nA 710 -58.40 -9.15 3.51e+01 1gdgA 293 -38.82 -9.12 3.55e+01 1cviA 342 -34.65 -9.11 3.56e+01 1avk 638 -58.57 -9.11 3.56e+01 1ckmA 330 -45.37 -9.10 3.58e+01 2u1a 88 -30.60 -9.03 3.68e+01 1hdmB 193 -34.95 -8.95 3.81e+01 1ja1A 622 -43.82 -8.93 3.84e+01 1jb7A 495 -41.68 -8.92 3.85e+01 2fivA 116 -32.36 -8.86 3.94e+01