% 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. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YEL010W.t2k-100-30-dssp-ehl2 Host: cc70 Mon Nov 11 06:30:02 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-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 117 nodes, 78.70 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(=1.5632) * Reverse)^tau(=0.8756))) % 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 1cviA 342 -33.09 -10.85 4.86e-02 2hpaA 342 -33.06 -10.81 5.05e-02 1fxoA 293 -28.80 -8.52 4.72e-01 1rpa 342 -31.57 -8.51 4.77e-01 1bet 107 -28.36 -8.50 4.80e-01 1quqB 121 -27.43 -7.84 9.31e-01 1g0rA 293 -27.43 -7.47 1.35e+00 1h5rA 293 -27.45 -7.00 2.16e+00 2pldA 105 -24.48 -6.71 2.90e+00 1d0nA 729 -29.23 -6.70 2.93e+00 1bia 321 -27.78 -6.46 3.76e+00 1bolA 222 -26.96 -6.33 4.31e+00 3vtk 343 -26.34 -6.13 5.30e+00 1g0uI 205 -27.66 -6.02 5.92e+00 1rypJ 204 -27.62 -5.98 6.15e+00 1dv1A 449 -27.38 -5.93 6.49e+00 1bncB 449 -27.36 -5.91 6.62e+00 1yagG 125 -24.70 -5.91 6.64e+00 1d4xG 126 -24.70 -5.90 6.70e+00 1gyxA 76 -22.68 -5.57 9.49e+00 1a6jA 163 -24.38 -5.45 1.07e+01 1d2kA 392 -27.02 -5.41 1.12e+01 1mai 131 -23.61 -5.36 1.18e+01 1k7wA 468 -27.00 -5.34 1.20e+01 1eg5A 384 -26.35 -5.31 1.24e+01 1bjx 110 -23.52 -5.26 1.31e+01 2bjxA 110 -23.52 -5.26 1.31e+01 2rslA 140 -23.51 -5.22 1.36e+01 1ecxA 384 -26.35 -5.19 1.40e+01 1kimA 366 -25.71 -5.18 1.42e+01 1dcnD 436 -26.85 -5.14 1.49e+01 2ki5A 366 -25.48 -4.98 1.76e+01 1qhiA 366 -25.48 -4.97 1.78e+01 1bib 321 -26.28 -4.96 1.79e+01 1a28A 256 -25.36 -4.87 1.97e+01 1auwA 468 -26.66 -4.87 1.98e+01 1fiwA 290 -26.07 -4.81 2.10e+01 1kamA 194 -23.88 -4.78 2.17e+01 1dpb 243 -24.48 -4.78 2.18e+01 2pleA 105 -21.90 -4.76 2.21e+01 1bncA 449 -26.12 -4.66 2.45e+01 1e1xA 299 -24.89 -4.62 2.56e+01 1hcl 298 -24.89 -4.62 2.57e+01 1bag 425 -25.61 -4.61 2.59e+01 2gatA 66 -20.40 -4.59 2.65e+01 3gatA 66 -20.40 -4.59 2.65e+01 1h99A 224 -25.60 -4.59 2.66e+01 1i50B 1224 -30.74 -4.56 2.75e+01 1dcnA 424 -25.85 -4.55 2.76e+01 1gatA 60 -20.11 -4.55 2.77e+01 1jvpP 298 -24.86 -4.51 2.91e+01 1rec 201 -24.50 -4.51 2.91e+01 1e2kA 331 -24.59 -4.50 2.92e+01 1a6wL 109 -23.35 -4.48 2.97e+01 1bcpF 99 -21.95 -4.48 2.98e+01 1irqA 71 -21.18 -4.47 3.03e+01 1uok 558 -26.31 -4.45 3.10e+01 3lck 271 -24.05 -4.44 3.12e+01 1fj2A 232 -24.67 -4.39 3.29e+01 1lox 662 -28.52 -4.39 3.31e+01 1f46A 140 -23.31 -4.36 3.42e+01 1prtF 98 -21.91 -4.35 3.44e+01 12asA 330 -24.37 -4.33 3.49e+01 1ji2A 585 -28.71 -4.33 3.51e+01 1iqaA 160 -23.52 -4.28 3.70e+01 1blxA 326 -24.96 -4.26 3.79e+01 1f47B 144 -23.31 -4.24 3.88e+01