% 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.YEL014C.t2k-100-30-dssp-ebghstl Host: cc64 Sat Dec 7 07:01:50 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YEL0/YEL014C % --------------------------------------------------------------------- % 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 YEL014C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YEL014C.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7458 sequences, 1753770 residues, 102 nodes, 70.12 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(=2.1732) * Reverse)^tau(=0.7705))) % 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 1i7dA 659 -31.70 -10.24 1.33e-01 1hlcA 129 -27.27 -7.41 1.48e+00 1qfxA 460 -30.46 -6.94 2.23e+00 1d6mA 653 -28.22 -6.88 2.36e+00 1eur 365 -28.42 -6.76 2.63e+00 1c8oA 300 -26.87 -6.09 4.87e+00 1f0cA 305 -27.06 -5.89 5.87e+00 1ky9B 448 -27.84 -5.83 6.18e+00 1cxvA 164 -25.34 -5.75 6.69e+00 830cA 168 -25.88 -5.72 6.85e+00 1ky9A 448 -27.70 -5.69 7.05e+00 4htcI 65 -22.93 -5.69 7.09e+00 1qhdA 398 -26.75 -5.30 1.02e+01 1h70A 255 -25.08 -5.28 1.04e+01 1h6fA 193 -25.53 -5.24 1.08e+01 1e7uA 961 -28.11 -5.23 1.09e+01 1eut 605 -28.90 -5.20 1.13e+01 1euu 605 -28.91 -4.98 1.39e+01 1idaA 99 -24.00 -4.94 1.44e+01 1dst 228 -25.76 -4.94 1.44e+01 1f97A 212 -25.88 -4.75 1.74e+01 1e6fA 143 -24.35 -4.72 1.79e+01 1ey2A 471 -28.66 -4.70 1.82e+01 1fhoA 119 -24.81 -4.68 1.85e+01 2bc2A 227 -25.07 -4.64 1.93e+01 1iicA 422 -27.19 -4.61 1.99e+01 1eybA 471 -28.66 -4.61 1.99e+01 2bc2B 227 -25.03 -4.60 2.00e+01 1k24A 253 -27.23 -4.54 2.14e+01 1ixmB 192 -23.36 -4.50 2.23e+01 1al0G 175 -24.75 -4.48 2.27e+01 1dcjA 81 -20.69 -4.47 2.29e+01 4sgbI 51 -20.95 -4.46 2.32e+01 1h95A 79 -22.63 -4.29 2.73e+01 1d7pM 159 -23.22 -4.29 2.75e+01 1g2iA 166 -23.16 -4.25 2.84e+01 1hg8A 349 -27.06 -4.25 2.85e+01 1jevA 517 -25.73 -4.23 2.91e+01 2olbA 517 -25.73 -4.22 2.94e+01 1ex7A 186 -23.71 -4.20 2.98e+01 1bxxA 285 -27.79 -4.19 3.02e+01 2bpa2 175 -24.96 -4.17 3.09e+01 1b8xA 280 -24.26 -4.15 3.15e+01 1c5yB 253 -24.89 -4.12 3.26e+01 2eifA 136 -25.32 -4.10 3.31e+01 1bet 107 -22.60 -4.10 3.32e+01 1lo7A 141 -23.00 -4.08 3.40e+01 1gj7B 253 -24.89 -4.07 3.41e+01 1korA 400 -25.02 -4.04 3.50e+01 1bio 228 -24.96 -4.02 3.57e+01 1fa8A 135 -22.66 -4.01 3.63e+01 1f9zA 135 -22.66 -3.99 3.69e+01 1ewfA 456 -25.77 -3.99 3.71e+01 1k9vF 201 -23.70 -3.98 3.74e+01 1d0dA 60 -20.66 -3.97 3.77e+01 1tap 60 -20.37 -3.97 3.78e+01 1gpwB 201 -23.69 -3.96 3.80e+01 1ll8A 114 -21.89 -3.95 3.84e+01 1bvqA 141 -22.68 -3.93 3.92e+01 1eaxA 241 -25.45 -3.93 3.94e+01