% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 09/03/03_16:30:36 % (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.YGR029W.t2k-100-30-dssp-ehl2 Host: cc57 Sat Oct 11 21:43:57 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR029W % --------------------------------------------------------------------- % 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 YGR029W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR029W.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8763 sequences, 2072585 residues, 190 nodes, 178.71 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(=2.6662) * Reverse)^tau(=0.7053))) % 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 1oqcA 125 -157.14 -132.86 4.29e-24 1jraA 117 -134.50 -112.49 4.51e-21 1jr8A 117 -134.36 -112.30 4.83e-21 1euvA 221 -32.84 -11.78 9.39e-02 1eyvA 156 -30.49 -11.39 1.23e-01 1ku1A 230 -30.68 -10.32 2.59e-01 1ngkA 128 -29.41 -9.93 3.42e-01 1p8cA 145 -29.79 -9.20 5.78e-01 1dgjA 907 -33.86 -8.77 7.96e-01 1iwhA 141 -27.39 -8.65 8.71e-01 1jjfA 268 -29.05 -7.68 1.82e+00 1ciy 590 -31.62 -7.51 2.06e+00 1cc8A 73 -23.97 -7.15 2.75e+00 1mhqA 148 -28.16 -6.87 3.44e+00 1fd8A 73 -23.50 -6.53 4.50e+00 1a32 88 -24.19 -6.40 5.01e+00 1je8A 82 -23.87 -6.28 5.53e+00 1okgA 373 -29.16 -6.24 5.72e+00 1agi 125 -24.87 -6.09 6.45e+00 1g4yR 148 -25.34 -6.04 6.71e+00 2abk 211 -26.17 -6.00 6.96e+00 1irdA 141 -24.91 -5.98 7.10e+00 2oneA 436 -27.78 -5.93 7.37e+00 1abwA 283 -26.37 -5.90 7.58e+00 1babA 143 -24.85 -5.84 7.95e+00 1j7yA 141 -24.84 -5.83 8.01e+00 1hlrA 907 -30.02 -5.73 8.68e+00 3cln 148 -25.46 -5.73 8.71e+00 1kyoD 248 -28.04 -5.70 8.97e+00 4enl 436 -27.59 -5.67 9.14e+00 1mlwA 301 -26.83 -5.61 9.68e+00 1o6eA 235 -26.11 -5.59 9.83e+00 1gio 125 -24.89 -5.58 9.88e+00 1ezvD 245 -27.99 -5.53 1.03e+01 1kb9D 246 -27.95 -5.53 1.03e+01 1iu8A 206 -25.44 -5.37 1.19e+01 1kw4A 89 -23.18 -5.36 1.19e+01 1dmhA 311 -27.10 -5.32 1.24e+01 1guzA 310 -25.89 -5.28 1.28e+01 1q8cA 151 -25.09 -5.24 1.32e+01 1esxA 96 -24.62 -5.07 1.53e+01 1jflA 228 -25.40 -5.03 1.59e+01 1mkaA 171 -25.12 -5.01 1.61e+01 1dw9A 156 -24.34 -4.97 1.68e+01 1dwkA 156 -24.18 -4.95 1.70e+01 1nn7A 105 -23.86 -4.93 1.73e+01 1g8iA 190 -25.39 -4.92 1.75e+01 1b9xB 68 -22.21 -4.89 1.80e+01 1m6bA 621 -29.21 -4.88 1.81e+01 1ysc 421 -26.74 -4.86 1.84e+01 1a04A 215 -25.22 -4.86 1.84e+01 4rnpA 883 -29.13 -4.80 1.94e+01 1hyeA 313 -25.29 -4.79 1.95e+01 1f6dA 376 -26.23 -4.79 1.96e+01 1myf 153 -24.50 -4.78 1.97e+01 1tbgE 68 -22.06 -4.77 2.00e+01 1cjwA 166 -24.53 -4.76 2.01e+01 1drtA 324 -25.53 -4.76 2.01e+01 1qovH 260 -27.68 -4.69 2.13e+01 1oneA 436 -26.25 -4.66 2.20e+01 1ystH 260 -28.41 -4.63 2.27e+01 1mg7A 417 -25.70 -4.62 2.29e+01 1sw6A 327 -26.35 -4.59 2.35e+01 1jwgA 147 -24.10 -4.58 2.36e+01 3kvt 115 -23.09 -4.56 2.41e+01 1pnkA 209 -24.48 -4.55 2.43e+01 1ngvA 534 -27.50 -4.52 2.50e+01 1iapA 211 -24.78 -4.52 2.51e+01 1ds1A 324 -25.26 -4.49 2.57e+01 1eyeA 280 -24.81 -4.46 2.63e+01 1gotG 73 -22.02 -4.45 2.66e+01 1i3zA 103 -22.52 -4.41 2.76e+01 1dryA 324 -25.25 -4.41 2.77e+01 1dwtA 153 -23.72 -4.39 2.80e+01 1gxqA 106 -22.52 -4.37 2.86e+01 1gjnA 153 -23.62 -4.31 3.01e+01 1ai7A 209 -24.29 -4.30 3.04e+01 1bw0A 416 -26.75 -4.26 3.16e+01 1fbmC 46 -20.92 -4.25 3.17e+01 1n9dA 199 -26.09 -4.25 3.20e+01 1be3D 241 -26.89 -4.25 3.20e+01 1ajqA 209 -24.19 -4.23 3.24e+01 1jvr 137 -31.47 -4.23 3.25e+01 1itg 166 -23.54 -4.23 3.25e+01 1dgmA 363 -24.79 -4.22 3.29e+01 1if1A 113 -24.46 -4.21 3.30e+01 1g8lA 411 -25.84 -4.18 3.41e+01 1b75A 94 -22.23 -4.17 3.43e+01 1f1eA 154 -22.95 -4.16 3.48e+01 1pyp 285 -28.57 -4.15 3.51e+01 1n9bA 265 -24.52 -4.13 3.56e+01 1ljrA 244 -26.55 -4.11 3.62e+01 1ee8A 266 -25.00 -4.11 3.63e+01 1iweA 457 -26.42 -4.10 3.64e+01 1jwhA 337 -25.70 -4.10 3.65e+01 1ko9A 345 -27.48 -4.10 3.66e+01 1pn1A 176 -23.99 -4.08 3.74e+01 1oxjA 173 -25.67 -4.06 3.80e+01 1e8nA 710 -26.74 -4.05 3.84e+01 1ilk 151 -23.94 -4.03 3.90e+01 1h2wA 710 -26.75 -4.02 3.93e+01 1qfmA 710 -26.75 -4.02 3.93e+01