% 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. % --------------------------------------------------------------------- % stridefoo.1.YBR217W.t2k-100-30-stride-ebghtl Host: farm16 Mon Nov 21 11:54:34 2005 % karplus Dir: /projects/compbiousr/compbio0404/experiments/protein-predict/yeast/YBR2/YBR217W % --------------------------------------------------------------------- % 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 +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YBR217W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YBR217W.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13086 sequences, 3100114 residues, 187 nodes, 287.05 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(=1.7548) * Reverse)^tau(=0.7316))) % 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 1gnuA 117 -119.94 -106.06 1.46e-16 1wz3A 96 -114.11 -103.03 3.80e-16 1kotA 119 -115.62 -102.43 4.59e-16 1eo6A 117 -81.77 -68.61 3.87e-11 1ugmA 125 -50.97 -38.14 4.31e-06 1l7yA 94 -24.67 -14.18 3.03e-01 2blcA 238 -21.83 -11.87 1.09e+00 2bl9A 238 -21.20 -11.52 1.33e+00 1dp4A 435 -21.23 -9.82 3.59e+00 1b2sD 90 -18.07 -9.15 5.38e+00 1ay7B 89 -17.75 -8.89 6.29e+00 1ge9A 184 -19.41 -8.86 6.42e+00 1vhsA 175 -18.84 -8.76 6.83e+00 1vd2A 89 -19.86 -8.66 7.27e+00 1mai 131 -18.41 -8.65 7.32e+00 1aqzA 149 -19.98 -8.62 7.46e+00 1cc8A 73 -17.70 -8.59 7.59e+00 1o51A 114 -18.70 -8.59 7.60e+00 1zo0A 126 -19.90 -8.54 7.85e+00 1az3A 244 -18.99 -8.47 8.17e+00 1j3kA 280 -18.35 -8.23 9.48e+00 1p80A 753 -21.04 -8.16 9.91e+00 1lsuA 147 -17.23 -8.04 1.07e+01 1cf9A 753 -20.90 -8.01 1.09e+01 1f8nA 839 -19.58 -7.91 1.16e+01 1fgqA 839 -19.51 -7.87 1.19e+01 1edzA 320 -20.70 -7.84 1.21e+01 1w5nA 337 -18.28 -7.82 1.23e+01 1i5gA 144 -17.61 -7.81 1.24e+01 1yge 839 -19.59 -7.79 1.25e+01 2a5yB 549 -17.97 -7.77 1.27e+01 1yqbA 100 -23.11 -7.75 1.29e+01 1yrgB 385 -17.68 -7.69 1.34e+01 1z2mA 155 -19.61 -7.66 1.36e+01 2aeaA 260 -20.43 -7.65 1.37e+01 1yrgA 385 -17.60 -7.63 1.39e+01 1f5nA 592 -17.62 -7.62 1.40e+01 1fd8A 73 -16.92 -7.61 1.40e+01 1wjnA 97 -20.74 -7.57 1.44e+01 1nf2A 268 -18.88 -7.56 1.45e+01 1j1lA 290 -18.49 -7.55 1.46e+01 1uqrA 154 -18.15 -7.54 1.47e+01 1aqzB 149 -17.97 -7.47 1.53e+01 1lfpA 249 -17.61 -7.33 1.68e+01 2apjA 260 -20.09 -7.32 1.70e+01 1vj0A 380 -17.18 -7.28 1.74e+01 1bd3A 243 -17.44 -7.23 1.80e+01 1ewxA 146 -18.90 -7.19 1.84e+01 1uh6A 100 -17.28 -7.18 1.86e+01 1oz9A 150 -18.32 -7.15 1.90e+01 1w5qA 337 -18.04 -7.07 1.99e+01 1z83A 196 -16.58 -7.06 2.01e+01 1pjcA 361 -17.37 -7.03 2.04e+01 1sa3A 262 -17.49 -7.00 2.09e+01 1wq3A 322 -16.93 -6.99 2.09e+01 1pjbA 361 -17.35 -6.99 2.10e+01 1qasA 622 -19.45 -6.99 2.10e+01 1hqsA 423 -18.13 -6.96 2.14e+01 1h8vA 218 -17.67 -6.95 2.16e+01 1yzfA 195 -17.98 -6.92 2.19e+01 1auyA 189 -16.27 -6.91 2.21e+01 1gr0A 367 -17.13 -6.91 2.22e+01 7catA 506 -18.63 -6.84 2.31e+01 1m3iA 471 -16.60 -6.84 2.31e+01 1nnjA 271 -16.34 -6.84 2.32e+01 1wvfA 520 -18.41 -6.83 2.33e+01 2rspA 124 -18.00 -6.83 2.33e+01 1lbeA 258 -17.27 -6.82 2.34e+01 1ew4A 106 -18.01 -6.81 2.37e+01 1fe0A 68 -16.92 -6.81 2.37e+01 1ab7 89 -16.06 -6.80 2.37e+01 1pf4A 582 -16.89 -6.79 2.40e+01 1s3sG 127 -18.57 -6.76 2.45e+01 1wba 175 -17.41 -6.75 2.45e+01 1k5dC 386 -16.83 -6.72 2.50e+01 1ee9A 320 -19.26 -6.69 2.56e+01 1wduA 245 -17.57 -6.66 2.60e+01 1brsD 89 -15.47 -6.59 2.73e+01 1vbkA 307 -19.02 -6.59 2.74e+01 1mvpA 124 -17.67 -6.58 2.75e+01 1o8xA 146 -17.85 -6.58 2.75e+01 1mmuA 347 -16.79 -6.55 2.81e+01 1oa2A 218 -17.40 -6.55 2.81e+01 1q52A 314 -17.28 -6.51 2.88e+01 1vjoA 393 -18.67 -6.49 2.92e+01 1nszA 347 -16.80 -6.49 2.93e+01 1d6mA 653 -17.01 -6.46 2.99e+01 1ihoA 283 -16.99 -6.44 3.02e+01 1sayA 361 -16.78 -6.44 3.02e+01 1l7jA 347 -16.79 -6.43 3.05e+01 1x72A 334 -17.95 -6.43 3.05e+01 1pl8A 356 -16.29 -6.42 3.06e+01 1xtoA 311 -18.87 -6.41 3.08e+01 1w3iA 293 -17.12 -6.40 3.10e+01 1pjjA 271 -15.99 -6.39 3.11e+01 1e08A 371 -16.81 -6.37 3.16e+01 1p3dA 475 -16.92 -6.37 3.16e+01 1qg7A 67 -16.18 -6.36 3.19e+01 1azsA 220 -16.29 -6.35 3.20e+01 1u1iA 392 -17.13 -6.33 3.26e+01 1gjwA 637 -17.72 -6.32 3.26e+01 1tdzA 272 -15.80 -6.29 3.33e+01 1o6jA 150 -16.29 -6.28 3.37e+01 1dzfA 215 -16.31 -6.27 3.38e+01 1ceo 343 -16.09 -6.25 3.44e+01 1f8gA 384 -16.32 -6.19 3.56e+01 1dghB 498 -17.31 -6.17 3.63e+01 1lurA 339 -16.73 -6.16 3.65e+01 1wmhA 89 -17.63 -6.15 3.66e+01 1h7nA 342 -16.57 -6.15 3.67e+01 1zr6A 503 -16.28 -6.15 3.68e+01 1ohlA 342 -16.57 -6.14 3.71e+01 1gzgA 337 -17.59 -6.12 3.75e+01 1upsA 420 -17.28 -6.11 3.76e+01 1up6A 416 -16.34 -6.11 3.78e+01 1l7jB 347 -16.27 -6.10 3.79e+01 1yfbA 59 -16.54 -6.10 3.80e+01 1k66A 149 -15.85 -6.08 3.85e+01 1kjwA 295 -16.14 -6.06 3.91e+01 1ylvA 342 -16.58 -6.04 3.95e+01 1zin 217 -15.23 -6.04 3.96e+01 1o0pA 104 -15.42 -6.03 3.98e+01