% 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.YGL228W.t2k-100-40-40-str2+CB_burial_14_7 Host: cc73 Sat Oct 11 21:33:29 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGL2/YGL228W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.str2s,/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 YGL228W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.400 File YGL228W.t2k.str2.mod % Track 2 FIMs added (the generic node (5)) % Track 2 Coeff 0.400 File YGL228W.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8763 sequences, 2072585 residues, 578 nodes, 597.27 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(=0.7554) * Reverse)^tau(=0.8357))) % 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 1qbqA 333 -70.01 -22.82 1.67e-01 1jcrA 377 -67.93 -22.80 1.68e-01 1d8dA 377 -68.43 -22.04 2.28e-01 1ft1A 377 -67.23 -21.56 2.76e-01 1h6qA 168 -61.55 -21.55 2.77e-01 1jcqA 382 -67.76 -21.27 3.09e-01 1ld8A 382 -67.64 -21.19 3.20e-01 1abwA 283 -61.06 -20.88 3.62e-01 1k8tA 510 -59.51 -19.52 6.26e-01 1pnkA 209 -66.81 -19.51 6.27e-01 1ge9A 184 -65.60 -17.18 1.63e+00 1a87 321 -56.41 -16.55 2.12e+00 1bj5 585 -61.19 -15.91 2.77e+00 1j1uA 306 -44.90 -15.79 2.91e+00 1ha2A 585 -59.16 -15.44 3.38e+00 1h6gA 256 -73.51 -15.42 3.40e+00 1sva1 361 -58.61 -15.36 3.50e+00 1ab4 477 -57.81 -15.17 3.79e+00 1ai7A 209 -61.64 -14.88 4.27e+00 1bjt 793 -64.87 -14.87 4.30e+00 1jfiB 179 -71.98 -14.85 4.33e+00 1n5uA 585 -55.39 -14.60 4.82e+00 1mp4A 292 -41.15 -14.53 4.96e+00 1h7sA 365 -44.68 -14.35 5.36e+00 1dg3A 592 -82.78 -14.24 5.63e+00 1pq9A 253 -50.43 -14.14 5.86e+00 1ku2A 241 -54.98 -13.89 6.52e+00 1dkgD 383 -43.53 -13.85 6.64e+00 2tct 207 -56.06 -13.70 7.07e+00 1dciA 275 -47.43 -13.24 8.64e+00 1bjz 207 -58.10 -13.20 8.77e+00 1fps 348 -47.56 -13.19 8.84e+00 1lvwA 295 -41.09 -13.13 9.06e+00 1flcB 175 -65.53 -12.88 1.01e+01 1jr3D 343 -51.79 -12.86 1.02e+01 1knyA 253 -47.36 -12.85 1.02e+01 1sly 618 -48.96 -12.75 1.07e+01 1hc7A 477 -43.33 -12.58 1.15e+01 1kx5D 125 -54.87 -12.43 1.23e+01 1jqjC 343 -44.64 -12.40 1.25e+01 1l8yA 91 -50.48 -12.39 1.25e+01 1orjA 130 -63.56 -12.24 1.33e+01 1colA 204 -46.95 -12.23 1.34e+01 1f5nA 592 -80.00 -12.20 1.35e+01 1ajqA 209 -60.66 -12.09 1.43e+01 1ofwA 296 -40.13 -12.06 1.44e+01 1an2A 86 -57.20 -12.04 1.45e+01 1jmuB 666 -54.18 -11.99 1.49e+01 1i4mA 108 -52.43 -11.98 1.49e+01 1jb0F 164 -50.26 -11.96 1.51e+01 1k99A 99 -51.69 -11.90 1.54e+01 1qsaA 618 -47.90 -11.88 1.56e+01 1eza 259 -54.56 -11.84 1.59e+01 1irdA 141 -45.96 -11.78 1.63e+01 1yghA 164 -39.04 -11.77 1.64e+01 1bs2A 607 -47.58 -11.51 1.84e+01 1cknA 330 -38.17 -11.49 1.85e+01 1bu7A 455 -46.09 -11.47 1.87e+01 1dw9A 156 -50.53 -11.47 1.87e+01 1fqvD 149 -49.64 -11.46 1.87e+01 1h38C 883 -51.51 -11.43 1.91e+01 1pxfA 111 -38.14 -11.41 1.92e+01 1el6A 219 -46.18 -11.39 1.94e+01 1i3dA 146 -47.77 -11.34 1.98e+01 1eduA 149 -45.21 -11.33 1.99e+01 1k8kD 300 -47.57 -11.33 1.99e+01 1sw6A 327 -40.97 -11.27 2.04e+01 1knvA 293 -43.60 -11.25 2.06e+01 1fa0A 537 -45.36 -11.19 2.12e+01 1gheA 177 -35.31 -11.14 2.16e+01 1kk6A 209 -38.15 -11.11 2.19e+01 1dx0A 219 -44.32 -11.07 2.23e+01 1bm9A 122 -51.75 -11.06 2.24e+01 1f9vA 347 -38.82 -11.06 2.25e+01 1ckmA 330 -38.81 -10.98 2.33e+01 1azo 232 -40.35 -10.96 2.35e+01 1fqvJ 149 -49.80 -10.93 2.38e+01 1g8iA 190 -54.15 -10.92 2.39e+01 1ft9A 222 -49.17 -10.91 2.39e+01 1bjx 110 -37.29 -10.91 2.39e+01 2bjxA 110 -37.29 -10.91 2.39e+01 1ovlA 271 -47.40 -10.90 2.41e+01 1g38A 393 -37.84 -10.90 2.41e+01 1cojA 212 -49.89 -10.86 2.46e+01 1oyjA 231 -45.40 -10.81 2.50e+01 1h5rA 293 -38.93 -10.80 2.52e+01 1bg1A 722 -73.40 -10.78 2.54e+01 1g5yA 238 -45.09 -10.77 2.55e+01 1l5pA 93 -34.86 -10.74 2.59e+01 1or7A 194 -64.47 -10.71 2.63e+01 1aqjA 421 -39.54 -10.70 2.63e+01 1mijA 152 -49.71 -10.63 2.71e+01 7catA 506 -53.89 -10.60 2.75e+01 1i6iA 366 -35.86 -10.58 2.78e+01 1hme 77 -47.51 -10.54 2.83e+01 1as4A 341 -38.40 -10.53 2.84e+01 1jeyA 609 -59.28 -10.53 2.84e+01 1fewA 184 -78.54 -10.51 2.87e+01 1sctB 151 -49.32 -10.49 2.89e+01 1dqeA 137 -40.97 -10.46 2.93e+01 1f0cA 305 -43.86 -10.44 2.96e+01 1k8kG 151 -46.18 -10.43 2.97e+01 1delA 241 -40.61 -10.36 3.06e+01 1mba 147 -48.44 -10.34 3.09e+01 2bmhA 455 -45.05 -10.33 3.11e+01 1nstA 325 -46.28 -10.31 3.13e+01 1dwkA 156 -50.96 -10.31 3.14e+01 1oq9A 363 -39.99 -10.28 3.17e+01 1dxrM 323 -61.16 -10.28 3.17e+01 1b0nA 111 -54.64 -10.26 3.20e+01 1n4kA 381 -44.55 -10.24 3.23e+01 1bjaA 95 -37.95 -10.23 3.25e+01 2cgpA 210 -47.08 -10.21 3.28e+01 1jpzA 473 -44.66 -10.17 3.34e+01 1a17 166 -54.82 -10.17 3.34e+01 2eiaB 206 -47.47 -10.16 3.35e+01 1el6B 219 -45.39 -10.16 3.36e+01 1i5rA 327 -40.10 -10.09 3.47e+01 2admA 421 -38.40 -10.08 3.47e+01 1uby 367 -45.67 -10.07 3.49e+01 1h0aA 158 -47.14 -9.99 3.63e+01 1ako 268 -34.04 -9.94 3.70e+01 3nodB 423 -44.26 -9.93 3.71e+01 1kyqA 274 -59.04 -9.91 3.76e+01 1dekA 241 -39.80 -9.89 3.78e+01 1ithA 141 -43.94 -9.89 3.78e+01 6prcM 323 -59.49 -9.88 3.80e+01 1h38D 883 -52.13 -9.84 3.87e+01 1fdt 327 -41.08 -9.77 4.00e+01