% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (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-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.YCR020W-B.t2k-100-30-CB_burial_14_7 Host: farm18 Mon Nov 29 11:47:49 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YCR0/YCR020W-B % --------------------------------------------------------------------- % 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 +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YCR020W-B.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YCR020W-B.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10944 sequences, 2597075 residues, 79 nodes, 85.70 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 (=10700) sequences: % N / (1 + exp(-(lambda(=1.9149) * Reverse)^tau(=0.7965))) % 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 1t07A 94 -22.54 -11.49 8.60e-02 1q06A 135 -25.62 -11.32 9.91e-02 1jbgA 109 -22.43 -10.74 1.59e-01 1ibzA 112 -19.42 -9.27 5.44e-01 1ibyA 112 -18.99 -9.14 6.07e-01 1aq5A 47 -21.94 -9.13 6.12e-01 1r5jA 337 -17.58 -8.90 7.46e-01 1i36A 264 -17.83 -8.36 1.19e+00 1tbmA 326 -17.67 -8.16 1.41e+00 1f2hA 169 -17.55 -7.25 3.16e+00 1dguA 183 -19.12 -7.24 3.18e+00 1kjyB 36 -17.96 -7.22 3.24e+00 1f3vA 179 -16.86 -7.19 3.34e+00 1wwbX 103 -17.84 -7.08 3.69e+00 1xa1A 255 -14.62 -6.83 4.62e+00 1dtx 59 -16.12 -6.79 4.75e+00 1kzuB 41 -16.90 -6.79 4.76e+00 1nkzB 41 -16.90 -6.79 4.76e+00 1sqeA 109 -16.71 -6.56 5.90e+00 1iznA 286 -16.11 -6.33 7.29e+00 1rifA 282 -16.07 -6.32 7.33e+00 1hy0A 466 -15.84 -6.29 7.52e+00 1bfi 112 -16.25 -6.27 7.68e+00 1pufA 77 -18.61 -6.06 9.34e+00 1v38A 78 -18.44 -6.00 9.81e+00 1dqiA 124 -16.40 -6.00 9.83e+00 1ge8A 249 -14.58 -5.98 1.01e+01 1iz5A 249 -14.44 -5.93 1.05e+01 1tz0A 114 -15.42 -5.85 1.13e+01 1l8cB 51 -18.35 -5.81 1.18e+01 1do6A 124 -16.30 -5.80 1.19e+01 1m4uA 206 -16.78 -5.78 1.21e+01 1etpA 190 -13.46 -5.74 1.25e+01 2hhmA 276 -13.27 -5.74 1.25e+01 1ub9A 100 -15.33 -5.72 1.28e+01 2pcdA 200 -15.35 -5.71 1.29e+01 3pcnA 200 -15.24 -5.68 1.32e+01 1i52A 236 -14.88 -5.66 1.34e+01 1imdA 277 -13.35 -5.65 1.37e+01 1h7sA 365 -15.28 -5.63 1.39e+01 1imbA 277 -13.19 -5.63 1.39e+01 1kd6A 179 -13.35 -5.60 1.43e+01 3pchA 200 -14.95 -5.58 1.46e+01 1unqA 125 -14.69 -5.51 1.55e+01 1pueE 89 -15.30 -5.44 1.66e+01 3pcgA 200 -14.98 -5.43 1.68e+01 1ijdB 42 -16.00 -5.38 1.75e+01 1m70A 190 -12.95 -5.38 1.75e+01 1t95A 240 -14.78 -5.37 1.78e+01 1mroC 247 -15.78 -5.36 1.80e+01 1xsvA 113 -16.81 -5.31 1.88e+01 1uilA 113 -14.60 -5.28 1.93e+01 1jmuB 666 -15.61 -5.25 1.98e+01 1es7B 89 -14.67 -5.25 1.99e+01 1hbnC 248 -15.54 -5.24 2.00e+01 1h10A 125 -14.36 -5.23 2.04e+01 1dpuA 99 -17.30 -5.22 2.05e+01 1g1cA 99 -13.30 -5.19 2.10e+01 1mq7A 154 -14.10 -5.17 2.15e+01 1si2A 149 -14.32 -5.13 2.24e+01 1bdo 80 -13.76 -5.09 2.31e+01 1m46A 148 -16.00 -5.03 2.46e+01 1ui0A 205 -12.69 -5.01 2.50e+01 1f46A 140 -13.62 -5.00 2.54e+01 1tzaA 134 -13.74 -4.96 2.62e+01 1lzlA 323 -13.04 -4.96 2.62e+01 1pvaA 110 -13.34 -4.96 2.63e+01 1np1A 184 -12.51 -4.85 2.92e+01 1gmiA 136 -13.22 -4.83 2.99e+01 1uetA 437 -14.55 -4.81 3.02e+01 1uaaA 673 -13.21 -4.80 3.06e+01 1lv3A 68 -15.33 -4.79 3.09e+01 1h9oA 112 -13.67 -4.77 3.17e+01 1g0uG 252 -13.22 -4.76 3.19e+01 1ufmA 84 -13.80 -4.75 3.23e+01 1ghqB 134 -13.27 -4.72 3.32e+01 1a68 95 -13.71 -4.72 3.33e+01 1kanA 253 -13.01 -4.67 3.47e+01 1r89A 437 -14.38 -4.66 3.52e+01 1exeA 99 -15.71 -4.65 3.55e+01 1ef1C 90 -18.78 -4.59 3.74e+01 1s5lU 134 -16.65 -4.56 3.86e+01 1iazA 179 -11.68 -4.55 3.91e+01 2tmkA 216 -13.85 -4.54 3.97e+01 1vheA 373 -14.12 -4.53 3.97e+01 1cs8A 316 -12.56 -4.53 3.99e+01