% 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. % --------------------------------------------------------------------- % alphafoo.1.YEL010W.t2k-100-30-alpha Host: cc70 Mon Nov 11 06:28:41 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.alphas % % 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.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 117 nodes, 79.08 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(=2.2758) * Reverse)^tau(=0.8279))) % 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 1bet 107 -27.15 -9.65 1.81e-02 1cviA 342 -31.12 -9.50 2.14e-02 2hpaA 342 -30.34 -8.83 4.51e-02 1rpa 342 -29.92 -8.33 7.97e-02 1hs6A 611 -30.36 -7.26 2.71e-01 1pcp 106 -23.74 -6.29 8.55e-01 1quqB 121 -24.29 -6.24 9.11e-01 1bjx 110 -24.31 -6.14 1.02e+00 2bjxA 110 -24.31 -6.14 1.02e+00 2pspA 106 -23.22 -6.02 1.17e+00 1bolA 222 -25.73 -6.02 1.18e+00 1uok 558 -27.11 -5.84 1.46e+00 1d2kA 392 -26.24 -5.67 1.80e+00 1ji2A 585 -27.63 -5.61 1.94e+00 1gyxA 76 -22.00 -5.51 2.19e+00 1a6wL 109 -23.25 -5.48 2.26e+00 1ecxA 384 -26.01 -5.47 2.30e+00 1g0uI 205 -25.04 -5.46 2.31e+00 487dL 133 -23.21 -5.34 2.70e+00 1bvzA 585 -27.53 -5.30 2.83e+00 1rypJ 204 -24.96 -5.28 2.90e+00 1eg5A 384 -25.77 -5.22 3.11e+00 1a6uL 108 -22.90 -5.15 3.40e+00 1dynA 125 -23.08 -5.14 3.46e+00 1hcl 298 -24.64 -5.07 3.74e+00 1i50B 1224 -29.10 -5.04 3.90e+00 1e1xA 299 -24.57 -4.97 4.25e+00 1gatA 60 -20.49 -4.89 4.67e+00 1kamA 194 -23.39 -4.86 4.86e+00 1mmsA 140 -22.92 -4.84 5.00e+00 1jvpP 298 -24.51 -4.83 5.06e+00 1irqA 71 -21.20 -4.80 5.24e+00 3gatA 66 -20.26 -4.57 6.96e+00 1fzvA 132 -24.21 -4.42 8.40e+00 2pldA 105 -21.68 -4.41 8.52e+00 1apa 266 -24.06 -4.40 8.67e+00 1dcnD 436 -24.96 -4.39 8.75e+00 1d0nA 729 -26.48 -4.37 8.97e+00 1a6jA 163 -22.77 -4.32 9.56e+00 2gatA 66 -20.01 -4.31 9.71e+00 1cczA 171 -23.36 -4.27 1.02e+01 1rec 201 -23.28 -4.24 1.06e+01 1hxs1 302 -23.65 -4.23 1.07e+01 1g0rA 293 -23.67 -4.21 1.10e+01 1j7dA 145 -22.38 -4.20 1.12e+01 1qp8A 303 -23.40 -4.19 1.14e+01 1ej6A 1289 -27.36 -4.18 1.15e+01 1k7wA 468 -24.85 -4.16 1.18e+01 1a8p 258 -23.45 -4.12 1.23e+01 2pleA 105 -21.06 -4.11 1.26e+01 1fxoA 293 -23.52 -4.10 1.27e+01 1fhoA 119 -22.41 -4.08 1.31e+01 1gm6A 175 -24.22 -4.05 1.35e+01 1cz4A 185 -22.94 -4.02 1.40e+01 1ew4A 106 -22.95 -3.97 1.49e+01 1e4mM 501 -25.08 -3.91 1.62e+01 1otgA 125 -21.49 -3.90 1.63e+01 1c8bA 371 -24.64 -3.90 1.64e+01 1bia 321 -24.00 -3.84 1.78e+01 1e6qM 501 -24.99 -3.82 1.82e+01 1rmg 422 -24.80 -3.82 1.83e+01 1e42A 258 -23.56 -3.78 1.92e+01 1bag 425 -24.35 -3.78 1.93e+01 1ds6B 180 -22.77 -3.76 1.97e+01 1lox 662 -26.38 -3.75 2.00e+01 1e70M 501 -24.93 -3.74 2.02e+01 1f3uB 171 -22.41 -3.73 2.05e+01 1j7iA 264 -23.71 -3.73 2.05e+01 1dm5A 315 -23.49 -3.73 2.06e+01 2pooA 355 -23.97 -3.69 2.16e+01 1bftA 101 -21.10 -3.69 2.16e+01 1fpzA 212 -23.10 -3.69 2.16e+01 1cs6A 382 -23.92 -3.68 2.18e+01 1irxA 523 -25.46 -3.68 2.18e+01 12asA 330 -23.20 -3.64 2.31e+01 1qlgA 355 -24.13 -3.64 2.31e+01 1jjfA 268 -24.05 -3.63 2.33e+01 2rslA 140 -21.52 -3.63 2.33e+01 1d4xG 126 -22.06 -3.63 2.35e+01 1tit 98 -21.15 -3.62 2.37e+01 1a8s 273 -22.87 -3.61 2.38e+01 1bib 321 -23.71 -3.60 2.43e+01 1dzrA 183 -23.00 -3.57 2.54e+01 1bk1 184 -22.73 -3.57 2.54e+01 1hnoA 280 -23.60 -3.56 2.54e+01 1bhjA 292 -23.56 -3.56 2.54e+01 1hqvA 191 -22.40 -3.56 2.57e+01 1qfoC 119 -21.61 -3.54 2.63e+01 2dynA 122 -21.61 -3.53 2.66e+01 1daqA 71 -19.60 -3.46 2.92e+01 1ah6 220 -22.83 -3.45 2.96e+01 1g2qA 187 -22.71 -3.45 2.97e+01 1a28A 256 -22.88 -3.44 2.98e+01 1hnuA 280 -23.44 -3.43 3.03e+01 1auwA 468 -24.26 -3.43 3.03e+01 1pov1 302 -23.28 -3.42 3.06e+01 1itvA 195 -22.04 -3.41 3.11e+01 1ecfA 504 -25.08 -3.39 3.22e+01 1cx8A 639 -25.27 -3.39 3.22e+01 1dpb 243 -22.97 -3.37 3.31e+01 1dcnA 424 -23.94 -3.36 3.31e+01 1xvaA 292 -23.36 -3.34 3.44e+01 1cx8B 639 -25.21 -3.30 3.62e+01 1f46A 140 -21.07 -3.28 3.70e+01 1iyjA 70 -19.67 -3.27 3.73e+01 1jl3A 139 -21.75 -3.27 3.74e+01 1cvmA 353 -23.74 -3.24 3.90e+01 1bxdA 161 -21.84 -3.23 3.95e+01