% 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. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YGR217W.t2k-100-30-dssp-ehl2 Host: cc85 Thu Feb 26 21:32:59 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.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 YGR217W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR217W.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 9381 sequences, 2218509 residues, 2040 nodes, 2596.45 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(=1.4671) * Reverse)^tau(=0.7493))) % 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 1ncx 162 -47.66 -24.53 3.53e-03 1top 162 -47.66 -24.53 3.53e-03 1jvmA 125 -40.50 -24.50 3.58e-03 1j95A 125 -40.68 -24.44 3.68e-03 1k4cC 124 -40.75 -24.08 4.31e-03 1r3jC 124 -40.75 -24.08 4.31e-03 1bl8A 97 -39.48 -24.08 4.33e-03 1t1dA 100 -36.32 -22.90 7.37e-03 3cln 148 -44.37 -21.62 1.33e-02 1ggzA 148 -46.52 -21.44 1.44e-02 1zac 90 -37.02 -20.43 2.31e-02 1g4yR 148 -41.21 -20.01 2.81e-02 1a68 95 -32.42 -19.68 3.28e-02 1avsA 90 -35.50 -19.19 4.14e-02 1cll 148 -45.54 -19.18 4.16e-02 1dsxA 87 -31.49 -18.88 4.80e-02 1kb9C 385 -54.54 -17.59 8.94e-02 1ezvC 385 -54.51 -17.50 9.33e-02 1exrA 148 -44.39 -16.76 1.34e-01 1byyA 53 -28.53 -16.36 1.64e-01 1kyoC 385 -53.60 -16.32 1.67e-01 1osa 148 -43.92 -15.94 2.02e-01 1iwgA 1053 -58.16 -15.74 2.22e-01 1j7rA 86 -29.77 -15.32 2.75e-01 2mysB 166 -33.50 -14.51 4.14e-01 1ho2A 20 -25.23 -14.43 4.32e-01 1oyeA 1049 -56.85 -14.39 4.41e-01 1nn7A 105 -27.07 -13.36 7.51e-01 1m46A 148 -28.40 -13.15 8.39e-01 1qg9A 21 -24.67 -12.97 9.22e-01 1lnh 857 -52.28 -12.96 9.24e-01 1wdcC 156 -31.00 -12.83 9.92e-01 1m45A 148 -28.15 -12.75 1.03e+00 1dceA 567 -39.03 -11.92 1.60e+00 1ehkA 562 -54.90 -11.84 1.68e+00 1jbaA 204 -29.35 -11.04 2.59e+00 1ezfA 340 -34.70 -10.78 2.99e+00 1jb0A 755 -43.00 -10.68 3.14e+00 1orsC 132 -38.80 -10.62 3.25e+00 1ggwA 140 -27.86 -10.48 3.53e+00 1aijL 281 -35.66 -10.24 4.02e+00 1o1fC 147 -29.16 -10.21 4.10e+00 1nr6A 473 -39.29 -10.11 4.33e+00 1q0sA 259 -27.95 -9.51 6.05e+00 1k9uA 78 -24.72 -9.41 6.40e+00 1wdcB 156 -28.40 -9.18 7.31e+00 1br1B 150 -27.81 -9.10 7.65e+00 1dhx 967 -53.62 -9.09 7.68e+00 2scpA 174 -25.95 -8.99 8.17e+00 1o86A 589 -33.81 -8.97 8.23e+00 1ctdA 36 -20.56 -8.68 9.76e+00 1n6bA 473 -37.39 -8.62 1.01e+01 1ctaA 36 -20.40 -8.61 1.02e+01 1gtxA 472 -33.96 -8.59 1.03e+01 1ohvA 472 -33.14 -8.29 1.22e+01 1ponA 36 -19.81 -8.23 1.27e+01 1dt6A 473 -38.22 -8.16 1.32e+01 1f0lA 535 -33.30 -8.02 1.44e+01 1pal 108 -22.21 -8.00 1.45e+01 1f5aA 513 -29.94 -7.91 1.53e+01 1f4qA 165 -26.24 -7.89 1.55e+01 1omrA 201 -27.72 -7.79 1.64e+01 1dcnD 436 -28.21 -7.79 1.65e+01 1ulmA 82 -24.25 -7.74 1.69e+01 1auwA 468 -28.59 -7.66 1.78e+01 1f0jA 377 -30.65 -7.65 1.79e+01 3kvt 115 -20.56 -7.63 1.81e+01 1be3C 379 -43.24 -7.56 1.88e+01 1gupA 348 -29.20 -7.49 1.97e+01 1ddt 535 -33.45 -7.45 2.01e+01 1n9dA 199 -27.26 -7.45 2.01e+01 1guqA 348 -29.05 -7.45 2.01e+01 1egdA 396 -32.61 -7.43 2.04e+01 1g8iA 190 -27.06 -7.39 2.09e+01 1wgtA 186 -30.78 -7.36 2.13e+01 2pvbA 107 -22.19 -7.32 2.19e+01 2liv 344 -28.07 -7.30 2.20e+01 1g5hA 454 -21.66 -7.24 2.29e+01 9wgaA 171 -28.03 -7.21 2.34e+01 1em2A 229 -20.66 -7.17 2.39e+01 1dcnA 424 -26.83 -7.15 2.43e+01 1drs 59 -22.72 -7.10 2.49e+01 2btvA 901 -32.90 -7.06 2.56e+01 1hev 43 -18.54 -7.03 2.61e+01 1i50A 1733 -78.05 -7.01 2.63e+01 1qvjA 292 -30.93 -6.99 2.66e+01 1b6a 478 -35.90 -6.99 2.67e+01 1upkA 341 -31.93 -6.95 2.74e+01 1mwvA 714 -37.66 -6.89 2.83e+01 1quvA 578 -26.70 -6.84 2.92e+01 1cdp 109 -20.81 -6.83 2.94e+01 1hxpA 348 -28.01 -6.77 3.06e+01 1e6fA 143 -20.81 -6.67 3.25e+01 1rec 201 -24.48 -6.66 3.27e+01 1phnA 162 -21.88 -6.61 3.38e+01 1ulkA 126 -25.71 -6.60 3.39e+01 1bn5 478 -35.86 -6.57 3.46e+01 1hcuA 503 -26.52 -6.57 3.46e+01 1q9bA 43 -17.90 -6.54 3.53e+01 1qs2A 401 -31.48 -6.48 3.64e+01 1qqfA 277 -24.88 -6.48 3.65e+01 1mmc 30 -18.63 -6.47 3.66e+01 1oohA 126 -22.54 -6.47 3.68e+01 1a28A 256 -24.61 -6.44 3.75e+01 1jpaA 312 -25.21 -6.42 3.80e+01 1txb 73 -22.72 -6.39 3.86e+01 1usgA 346 -29.49 -6.39 3.87e+01 1gx5A 536 -26.46 -6.35 3.96e+01 1c3cA 429 -28.47 -6.34 3.98e+01