% 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. % --------------------------------------------------------------------- % CB_burial_14_7foo.1.YGR029W.t2k-100-30-CB_burial_14_7 Host: cc57 Sat Oct 11 21:49:57 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.CB-burial-14-7s % % 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.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8763 sequences, 2072585 residues, 190 nodes, 179.73 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(=1.8640) * Reverse)^tau(=0.8033))) % 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 -144.10 -117.66 8.48e-30 1jr8A 117 -122.69 -96.67 5.56e-25 1jraA 117 -121.87 -95.15 1.26e-24 1qovH 260 -40.39 -11.55 6.32e-02 1ystH 260 -41.37 -11.23 8.21e-02 1i7fA 292 -34.78 -8.18 1.09e+00 1kb9C 385 -28.94 -7.73 1.62e+00 1ezvC 385 -28.78 -7.53 1.93e+00 2trcP 217 -35.67 -7.23 2.53e+00 1eyvA 156 -27.45 -7.13 2.76e+00 1kyoC 385 -28.30 -7.03 3.02e+00 1eyeA 280 -27.44 -6.99 3.15e+00 1b75A 94 -27.17 -6.97 3.19e+00 1dfuP 94 -27.12 -6.82 3.66e+00 1i3zA 103 -27.03 -6.82 3.66e+00 1iwhA 141 -26.41 -6.79 3.75e+00 1evsA 187 -29.61 -6.66 4.22e+00 1cg5B 141 -26.28 -6.51 4.86e+00 1hw7A 255 -32.47 -6.12 6.96e+00 1ngkA 128 -27.15 -5.98 7.93e+00 1jnuA 104 -27.52 -5.48 1.27e+01 1g8lA 411 -27.36 -5.38 1.39e+01 1ciy 590 -27.65 -5.10 1.81e+01 1euvA 221 -26.47 -5.09 1.83e+01 1cr1A 296 -27.96 -5.08 1.85e+01 1fxrA 64 -24.50 -5.04 1.92e+01 1fd8A 73 -24.56 -5.04 1.92e+01 3hmgB 175 -34.44 -5.03 1.95e+01 1ldjB 90 -26.88 -5.02 1.96e+01 1cr0A 296 -27.77 -4.88 2.25e+01 2viuB 175 -34.12 -4.88 2.26e+01 1skz 119 -30.30 -4.87 2.28e+01 1pdnC 128 -32.67 -4.84 2.35e+01 1fjxA 327 -26.45 -4.80 2.43e+01 1loi 26 -22.04 -4.73 2.60e+01 1hgeB 175 -34.09 -4.70 2.69e+01 1dfd 64 -23.58 -4.62 2.88e+01 1hmy 327 -27.25 -4.57 3.05e+01 1cch 82 -26.53 -4.56 3.06e+01 1iapA 211 -26.90 -4.51 3.23e+01 1urk 130 -28.21 -4.46 3.38e+01 1b35C 282 -32.37 -4.41 3.57e+01 1h4rA 314 -26.63 -4.39 3.64e+01 2abk 211 -24.84 -4.38 3.66e+01 1cc8A 73 -24.30 -4.38 3.67e+01 1ngvA 534 -28.58 -4.36 3.73e+01 1babA 143 -23.90 -4.36 3.75e+01 3mhtA 327 -26.68 -4.34 3.81e+01 1jj2P 95 -29.25 -4.33 3.87e+01 1j75A 67 -25.89 -4.32 3.91e+01