% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 07/18/05_14:54:13 % (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.YEL012W.t2k-100-30-CB_burial_14_7 Host: farm09 Fri Nov 18 19:52:01 2005 % karplus Dir: /projects/compbiousr/compbio0404/experiments/protein-predict/yeast/YEL0/YEL012W % --------------------------------------------------------------------- % 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 YEL012W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YEL012W.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13048 sequences, 3092733 residues, 219 nodes, 339.36 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 (10000.00) % E-value on N (=11000) sequences: % N / (1 + exp(-(lambda(=1.4434) * Reverse)^tau(=0.8346))) % Calculated when Simple < simple_threshold (10000.00) % 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 1z2uA 150 -195.00 -180.66 8.16e-42 1x23A 155 -190.15 -179.02 1.79e-41 2ayvA 166 -187.78 -176.31 6.61e-41 1y6lA 149 -178.99 -168.64 2.71e-39 1jbbA 153 -175.38 -163.52 3.27e-38 1jatA 155 -174.49 -163.12 3.98e-38 2bepA 159 -167.58 -156.59 9.76e-37 1yh2A 175 -165.74 -154.92 2.22e-36 1u9aA 160 -166.48 -153.93 3.61e-36 1fzyA 149 -164.30 -153.09 5.47e-36 2e2c 156 -165.08 -152.29 8.10e-36 1fxtA 149 -162.12 -151.44 1.24e-35 2ucz 165 -165.19 -150.76 1.73e-35 1i7kA 179 -156.58 -144.95 3.09e-34 1zdnA 158 -152.76 -141.61 1.63e-33 1yh6A 179 -150.29 -137.08 1.58e-32 1yf9A 171 -144.67 -133.29 1.07e-31 1wzvA 155 -140.04 -127.77 1.75e-30 1yrvA 169 -135.73 -123.46 1.58e-29 2awfA 172 -135.34 -121.47 4.36e-29 2a4dA 160 -123.80 -112.58 4.26e-27 1j7dA 145 -120.35 -106.96 8.00e-26 1jatB 138 -118.55 -104.91 2.35e-25 1zuoA 186 -81.33 -68.52 8.90e-17 1s1qA 145 -32.10 -20.40 5.39e-04 1kppA 145 -31.38 -19.40 1.08e-03 1lj9A 144 -32.34 -15.91 1.26e-02 1uzxA 169 -27.56 -13.39 7.91e-02 1xpjA 126 -26.36 -12.79 1.24e-01 2es9A 115 -22.95 -12.33 1.73e-01 2a9uA 144 -31.94 -11.70 2.80e-01 1sd4A 126 -29.29 -10.61 6.38e-01 1ywzA 175 -23.90 -10.55 6.71e-01 1ovqA 138 -23.89 -10.42 7.38e-01 2biiA 424 -20.28 -10.42 7.41e-01 1nu0A 138 -21.40 -9.49 1.53e+00 1on2A 142 -24.13 -8.83 2.56e+00 1winA 143 -22.79 -8.82 2.57e+00 1w33A 181 -24.02 -8.65 2.94e+00 1s7oA 113 -25.09 -8.45 3.44e+00 1ucyH 150 -22.32 -8.43 3.52e+00 1o5oA 221 -19.59 -8.24 4.09e+00 1ks8A 433 -16.27 -7.92 5.30e+00 1ryc 294 -17.37 -7.81 5.77e+00 1br0A 120 -26.33 -7.79 5.86e+00 1lxnA 99 -20.29 -7.46 7.66e+00 1y7rA 133 -18.62 -7.37 8.26e+00 1lnwA 147 -21.93 -7.35 8.36e+00 2a61A 145 -25.23 -7.31 8.69e+00 1ukxA 137 -21.28 -7.26 9.03e+00 1v9sA 208 -17.96 -7.22 9.32e+00 1dd5A 185 -23.70 -7.18 9.59e+00 1i8kB 124 -16.04 -7.17 9.71e+00 1t3wA 148 -28.22 -7.10 1.03e+01 1bihA 395 -17.16 -7.09 1.04e+01 1fqvJ 149 -22.45 -7.05 1.07e+01 1uedA 406 -17.94 -7.02 1.10e+01 1eyvA 156 -17.57 -7.02 1.10e+01 1s7mA 174 -27.24 -7.00 1.12e+01 1fewA 184 -22.40 -6.78 1.34e+01 1eqfA 280 -20.00 -6.73 1.40e+01 1wlmA 151 -23.26 -6.68 1.45e+01 1qqcA 773 -18.88 -6.67 1.47e+01 1ykhA 108 -26.03 -6.64 1.50e+01 1ez3A 127 -24.76 -6.59 1.56e+01 2aobA 99 -24.16 -6.58 1.58e+01 1iv8A 720 -17.88 -6.54 1.63e+01 2a6qA 86 -24.43 -6.50 1.69e+01 1wm3A 72 -19.09 -6.45 1.75e+01 1n4kA 381 -17.82 -6.44 1.78e+01 1gh6A 114 -23.52 -6.43 1.79e+01 2nllB 103 -20.77 -6.41 1.82e+01 1bg1A 722 -20.22 -6.39 1.85e+01 1fc3A 120 -18.16 -6.38 1.87e+01 1pcfA 66 -23.43 -6.30 2.00e+01 1h3fA 432 -18.67 -6.26 2.05e+01 1vfaB 116 -16.01 -6.25 2.08e+01 1v63A 101 -24.66 -6.25 2.09e+01 1okrA 123 -24.16 -6.22 2.13e+01 1h9dB 134 -17.05 -6.18 2.21e+01 1oyjA 231 -15.77 -6.14 2.27e+01 1ccg 291 -15.36 -6.13 2.29e+01 1lv3A 68 -22.97 -6.12 2.31e+01 1fqvD 149 -21.56 -6.10 2.35e+01 1hs6A 611 -16.19 -6.09 2.37e+01 1g7jB 116 -15.67 -6.09 2.38e+01 1dseA 292 -14.97 -5.99 2.58e+01 1e50B 134 -16.79 -5.98 2.60e+01 1om2A 95 -21.64 -5.98 2.60e+01 1pszA 303 -16.17 -5.97 2.62e+01 1jb0D 138 -22.68 -5.97 2.64e+01 2astA 159 -21.45 -5.96 2.65e+01 2hmqA 113 -18.67 -5.96 2.66e+01 1ggwA 140 -20.52 -5.95 2.67e+01 1jb1A 205 -19.48 -5.91 2.76e+01 1ajyA 71 -22.70 -5.90 2.78e+01 1ibjA 464 -17.42 -5.90 2.79e+01 1uyrA 737 -21.69 -5.86 2.89e+01 2hmzA 113 -18.68 -5.81 3.01e+01 1iyjA 70 -26.37 -5.81 3.01e+01 1a17 166 -22.82 -5.80 3.03e+01 1kewA 361 -15.13 -5.79 3.05e+01 1e0fI 57 -20.68 -5.78 3.08e+01 1zmbA 290 -18.31 -5.78 3.09e+01 1jsqA 582 -20.96 -5.78 3.09e+01 1nzyA 269 -19.57 -5.76 3.13e+01 2ar0A 541 -21.34 -5.74 3.19e+01 1is1A 185 -18.47 -5.73 3.21e+01 1ds4A 292 -14.76 -5.73 3.21e+01 1ux8A 132 -18.47 -5.69 3.34e+01 1a0fA 201 -17.05 -5.66 3.41e+01 1nuyA 337 -14.57 -5.63 3.50e+01 1c4kA 730 -16.68 -5.61 3.56e+01 1f2tB 148 -18.77 -5.59 3.63e+01 1ieaA 192 -22.58 -5.57 3.68e+01 1bcsA 263 -19.22 -5.57 3.69e+01 1d7qA 143 -26.24 -5.54 3.78e+01 1z53A 294 -14.68 -5.52 3.84e+01 1r7jA 95 -19.96 -5.50 3.91e+01 1ni4A 365 -18.27 -5.50 3.92e+01