% 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. % --------------------------------------------------------------------- % stridefoo.1.YGR029W.t2k-100-30-stride-ebghtl Host: cc57 Sat Oct 11 21:34:55 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.2ds % % 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.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8763 sequences, 2072585 residues, 190 nodes, 178.81 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(=2.3498) * Reverse)^tau(=0.7017))) % 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 -163.38 -139.49 4.22e-22 1jr8A 117 -138.70 -116.34 4.45e-19 1jraA 117 -137.23 -114.44 8.02e-19 1eyvA 156 -30.46 -11.57 3.19e-01 1euvA 221 -33.10 -10.59 5.87e-01 1p8cA 145 -30.89 -10.20 7.51e-01 1ngkA 128 -28.89 -10.00 8.53e-01 1jvr 137 -33.12 -9.97 8.74e-01 1dgjA 907 -33.96 -9.47 1.21e+00 1ku1A 230 -29.37 -9.09 1.55e+00 1mlwA 301 -29.98 -8.89 1.77e+00 1ciy 590 -31.76 -8.20 2.82e+00 1iwhA 141 -27.28 -8.10 3.02e+00 1a32 88 -25.73 -7.77 3.79e+00 1je8A 82 -25.15 -7.44 4.77e+00 1agi 125 -25.77 -7.32 5.18e+00 1hlrA 907 -31.92 -7.29 5.29e+00 4enl 436 -29.01 -7.21 5.58e+00 1cc8A 73 -23.89 -7.09 6.10e+00 2abk 211 -27.11 -7.02 6.40e+00 1jwhA 337 -30.20 -6.95 6.75e+00 1g8iA 190 -26.83 -6.95 6.76e+00 1hyvA 166 -25.61 -6.90 7.00e+00 1jjfA 268 -28.04 -6.89 7.04e+00 1abwA 283 -27.44 -6.75 7.77e+00 1j7yA 141 -25.97 -6.75 7.81e+00 1babA 143 -25.98 -6.72 7.94e+00 1oneA 436 -28.34 -6.65 8.39e+00 1jenB 67 -24.07 -6.64 8.44e+00 1ha2A 585 -29.71 -6.49 9.40e+00 1b9dA 163 -25.10 -6.46 9.58e+00 1pov1 302 -28.52 -6.26 1.11e+01 1gg3A 279 -28.14 -6.23 1.14e+01 1g4yR 148 -24.77 -6.22 1.14e+01 1m2rA 327 -27.74 -6.22 1.15e+01 1kyoD 248 -28.29 -6.20 1.16e+01 1bev1 281 -28.14 -6.20 1.16e+01 1toh 343 -27.08 -6.15 1.20e+01 1if1A 113 -25.40 -6.13 1.22e+01 1kb9D 246 -28.41 -6.09 1.27e+01 1tbgE 68 -23.30 -5.99 1.36e+01 1gotG 73 -23.51 -5.99 1.36e+01 1okgA 373 -27.53 -5.87 1.48e+01 1o6eA 235 -26.00 -5.86 1.50e+01 1be3D 241 -28.11 -5.79 1.59e+01 2sas 185 -25.30 -5.73 1.65e+01 1qhtA 775 -28.32 -5.73 1.66e+01 1qopB 396 -27.80 -5.70 1.70e+01 1a04A 215 -26.27 -5.69 1.71e+01 1bl3A 160 -24.22 -5.63 1.79e+01 1o2dA 371 -27.31 -5.55 1.89e+01 1j5rA 371 -27.31 -5.55 1.89e+01 1pbwA 216 -26.39 -5.55 1.90e+01 1fxxA 482 -27.69 -5.53 1.93e+01 1cs1A 386 -26.68 -5.52 1.94e+01 1b9xB 68 -22.95 -5.51 1.95e+01 1phd 414 -27.59 -5.48 2.01e+01 2occM 46 -23.22 -5.47 2.02e+01 1d5rA 324 -25.96 -5.45 2.04e+01 1q8cA 151 -25.61 -5.44 2.06e+01 1hzfA 367 -26.91 -5.36 2.20e+01 1ezvD 245 -28.40 -5.36 2.20e+01 1bj5 585 -28.74 -5.31 2.28e+01 1g8lA 411 -26.84 -5.30 2.29e+01 1gio 125 -23.57 -5.29 2.32e+01 1k8yB 396 -27.40 -5.27 2.35e+01 1tgoA 773 -28.08 -5.23 2.43e+01 1itg 166 -24.55 -5.20 2.48e+01 1e7aA 585 -28.70 -5.20 2.48e+01 1n5uA 585 -28.67 -5.07 2.76e+01 1hbyA 123 -23.82 -5.06 2.77e+01 1ao6A 585 -28.71 -5.06 2.77e+01 1ibjA 464 -28.51 -5.06 2.78e+01 1ppfE 218 -26.57 -5.04 2.82e+01 1esxA 96 -24.84 -4.99 2.92e+01 1cjwA 166 -24.94 -4.94 3.04e+01 1iufA 144 -24.41 -4.93 3.06e+01 1j8uA 325 -28.01 -4.89 3.16e+01 1jj2L 194 -26.35 -4.89 3.16e+01 1ac5 483 -29.24 -4.85 3.27e+01 1jfvA 131 -24.70 -4.85 3.28e+01 1k59A 123 -23.81 -4.82 3.36e+01 1mqvA 125 -23.84 -4.81 3.39e+01 1dxsA 80 -24.13 -4.80 3.42e+01 1m6bA 621 -31.03 -4.79 3.43e+01 2itg 163 -23.76 -4.78 3.46e+01 1ysc 421 -26.90 -4.76 3.51e+01 1jwwA 80 -21.78 -4.76 3.52e+01 1ljrA 244 -28.12 -4.75 3.55e+01 1sw6A 327 -26.37 -4.74 3.57e+01 1mhqA 148 -26.70 -4.73 3.59e+01 1fd8A 73 -21.61 -4.73 3.60e+01 1j5sA 463 -27.11 -4.71 3.66e+01 1fa4A 105 -24.51 -4.71 3.67e+01 1ystH 260 -29.36 -4.70 3.68e+01 1dwtA 153 -24.25 -4.70 3.68e+01 7aatA 401 -25.65 -4.70 3.70e+01 1ez3A 127 -24.00 -4.70 3.70e+01 1o98A 511 -27.42 -4.68 3.75e+01 2tysB 397 -26.96 -4.68 3.76e+01 1gjnA 153 -24.13 -4.66 3.81e+01 1mkaA 171 -24.56 -4.66 3.81e+01 1ejjA 511 -27.24 -4.64 3.87e+01 1fr2B 134 -24.00 -4.64 3.89e+01 1oxjA 173 -25.79 -4.64 3.89e+01 1phg 414 -26.74 -4.62 3.93e+01 1cs1C 386 -26.03 -4.62 3.94e+01 1dw9A 156 -23.83 -4.61 3.96e+01 1dwkA 156 -23.83 -4.61 3.96e+01 1a7vA 125 -23.59 -4.61 3.97e+01 1qsaA 618 -26.87 -4.60 3.99e+01