% 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. % --------------------------------------------------------------------- % dsspfoo.1.YEL010W.t2k-100-30-dssp-ebghstl Host: cc70 Mon Nov 11 06:25:55 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YEL0/YEL010W % --------------------------------------------------------------------- % 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 ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YEL010W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YEL010W.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 117 nodes, 79.00 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(=1.4864) * Reverse)^tau(=0.8729))) % 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 2hpaA 342 -34.09 -11.88 3.46e-02 1cviA 342 -34.02 -11.78 3.79e-02 1rpa 342 -32.78 -9.29 3.69e-01 1quqB 121 -28.62 -9.10 4.40e-01 1bet 107 -28.92 -8.97 5.00e-01 1fxoA 293 -28.88 -8.50 7.77e-01 1d0nA 729 -29.84 -7.39 2.22e+00 1bolA 222 -28.00 -7.36 2.28e+00 1h5rA 293 -27.69 -7.16 2.77e+00 1g0rA 293 -27.07 -7.10 2.93e+00 2pldA 105 -25.09 -7.01 3.20e+00 1yagG 125 -25.37 -6.70 4.32e+00 1a6jA 163 -25.65 -6.43 5.61e+00 1d4xG 126 -25.12 -6.40 5.74e+00 1bncB 449 -27.60 -6.19 7.05e+00 1bia 321 -27.43 -6.15 7.33e+00 1dv1A 449 -27.62 -6.12 7.62e+00 1dqaA 467 -27.34 -6.04 8.18e+00 1hs6A 611 -31.77 -5.93 9.13e+00 1hw8A 467 -27.39 -5.90 9.41e+00 1bib 321 -27.16 -5.82 1.02e+01 1dqaC 467 -27.22 -5.81 1.03e+01 1ecxA 384 -26.86 -5.73 1.12e+01 3vtk 343 -26.36 -5.61 1.25e+01 1eg5A 384 -26.52 -5.53 1.36e+01 1mai 131 -23.71 -5.46 1.45e+01 1a6wL 109 -24.37 -5.30 1.71e+01 1h99A 224 -25.90 -5.27 1.75e+01 1bag 425 -26.25 -5.24 1.81e+01 1gyxA 76 -22.63 -5.19 1.90e+01 12asA 330 -25.24 -5.16 1.95e+01 2pleA 105 -22.28 -5.13 2.01e+01 1g0uI 205 -27.13 -5.10 2.08e+01 1bcpF 99 -22.62 -5.10 2.08e+01 1rypJ 204 -27.08 -5.03 2.22e+01 1d2kA 392 -26.99 -5.02 2.26e+01 1jjfA 268 -26.45 -5.01 2.27e+01 1uok 558 -26.85 -5.01 2.28e+01 1k7wA 468 -26.93 -5.01 2.28e+01 1ig8A 486 -27.49 -4.99 2.33e+01 1dcnD 436 -26.90 -4.98 2.35e+01 1im8A 244 -25.10 -4.95 2.42e+01 1bncA 449 -26.45 -4.94 2.43e+01 1kbhB 59 -21.71 -4.92 2.49e+01 1ji2A 585 -29.68 -4.90 2.53e+01 1lbvA 252 -24.82 -4.89 2.56e+01 1bjx 110 -23.20 -4.88 2.60e+01 2bjxA 110 -23.20 -4.88 2.60e+01 1a6uL 108 -23.82 -4.83 2.72e+01 1prtF 98 -22.34 -4.78 2.87e+01 1gatA 60 -20.25 -4.78 2.88e+01 1daqA 71 -22.21 -4.77 2.88e+01 1a28A 256 -25.84 -4.76 2.93e+01 3gatA 66 -20.47 -4.74 3.00e+01 1iqaA 160 -24.19 -4.73 3.01e+01 1ah6 220 -25.26 -4.72 3.04e+01 2gatA 66 -20.41 -4.69 3.13e+01 1g5aA 628 -27.19 -4.69 3.13e+01 1fzvA 132 -27.91 -4.68 3.17e+01 1gdtA 183 -26.05 -4.65 3.27e+01 1fl7B 111 -25.32 -4.63 3.33e+01 1vppV 102 -25.44 -4.60 3.43e+01 1auwA 468 -26.63 -4.58 3.49e+01 1cy5A 97 -22.34 -4.58 3.51e+01 1fltV 98 -25.30 -4.56 3.59e+01 1qp8A 303 -24.14 -4.54 3.67e+01 1irqA 71 -21.43 -4.54 3.67e+01 1f3uB 171 -24.23 -4.53 3.71e+01 1i50B 1224 -31.13 -4.52 3.74e+01 1a1d 146 -22.45 -4.46 3.98e+01