% 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. % --------------------------------------------------------------------- % dsspfoo.1.YGL228W.t2k-100-30-dssp-ebghstl Host: cc73 Sat Oct 11 20:11:16 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.dssps % % 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 0.300 File YGL228W.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8763 sequences, 2072585 residues, 578 nodes, 555.98 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(=1.3961) * Reverse)^tau(=0.7490))) % 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 1h5rA 293 -39.61 -16.65 2.13e-01 1abwA 283 -42.94 -15.74 3.29e-01 1mp4A 292 -37.07 -14.39 6.37e-01 1gw5M 435 -35.97 -11.45 2.81e+00 1lvwA 295 -34.27 -11.25 3.13e+00 1h4vB 421 -34.71 -10.51 4.63e+00 1jk0A 419 -44.71 -10.50 4.65e+00 1p5zB 263 -36.08 -10.34 5.06e+00 1colA 204 -40.86 -10.33 5.09e+00 1hz4A 373 -41.52 -10.07 5.85e+00 1t7pA 698 -41.68 -9.70 7.13e+00 1adjA 421 -33.68 -9.69 7.19e+00 1ki1B 352 -41.02 -9.67 7.26e+00 1bg1A 722 -51.91 -9.49 7.99e+00 1qsaA 618 -37.63 -9.18 9.51e+00 1kfiA 572 -35.55 -9.14 9.73e+00 1lkxA 697 -39.22 -9.08 1.00e+01 1sly 618 -37.08 -8.83 1.15e+01 1dpjA 329 -35.07 -8.69 1.24e+01 1j1uA 306 -34.00 -8.62 1.30e+01 1ab4 477 -38.77 -8.51 1.38e+01 1mhyB 395 -41.38 -8.42 1.45e+01 1oyjA 231 -34.66 -8.42 1.45e+01 1jqeA 292 -32.44 -8.40 1.47e+01 1h0oA 390 -40.22 -8.30 1.55e+01 1nt2B 258 -42.08 -8.18 1.66e+01 1gqiA 708 -35.79 -8.12 1.72e+01 1qciA 262 -33.42 -8.05 1.79e+01 1lp4A 332 -31.55 -7.97 1.86e+01 1orjA 130 -39.20 -7.96 1.87e+01 1m2rA 327 -31.50 -7.95 1.89e+01 1lpuA 332 -31.54 -7.95 1.89e+01 1a87 321 -38.96 -7.94 1.91e+01 1m4jA 142 -28.77 -7.91 1.94e+01 1bh9B 89 -32.25 -7.84 2.02e+01 1xsm 390 -38.86 -7.82 2.03e+01 1d6aB 262 -32.59 -7.74 2.13e+01 1fi4A 416 -34.68 -7.70 2.19e+01 1l8aA 886 -35.54 -7.56 2.37e+01 1h6pA 203 -36.34 -7.55 2.38e+01 1oheA 348 -32.19 -7.50 2.44e+01 1hc7A 477 -32.77 -7.43 2.54e+01 1pjr 724 -39.66 -7.42 2.57e+01 1dlc 584 -39.91 -7.40 2.59e+01 1fewA 184 -38.97 -7.38 2.62e+01 1fxoA 293 -30.03 -7.37 2.64e+01 1mmoD 512 -37.53 -7.30 2.75e+01 1afrA 345 -38.54 -7.27 2.80e+01 1qoyA 318 -44.81 -7.25 2.83e+01 1vom 762 -35.17 -7.20 2.91e+01 1k4wA 252 -33.35 -7.18 2.95e+01 1ldg 316 -31.61 -7.16 2.98e+01 2cblA 305 -35.23 -7.14 3.02e+01 1irxA 523 -34.35 -7.13 3.04e+01 1b47A 304 -35.02 -7.11 3.07e+01 1p80A 753 -32.99 -7.10 3.09e+01 1h6gA 256 -45.58 -7.06 3.17e+01 1n7oA 721 -38.25 -7.00 3.28e+01 2wrpR 107 -30.97 -6.99 3.29e+01 1hstA 90 -26.86 -6.97 3.33e+01 1div 149 -33.49 -6.96 3.36e+01 3csuA 310 -29.56 -6.94 3.40e+01 1nq7A 244 -33.92 -6.92 3.42e+01 1a9xA 1058 -33.59 -6.90 3.47e+01 1lxkA 721 -38.95 -6.90 3.47e+01 2ki5A 366 -31.65 -6.89 3.49e+01 1at1A 310 -29.36 -6.83 3.62e+01 1g4yR 148 -28.96 -6.83 3.63e+01 1kpgA 287 -30.97 -6.81 3.67e+01 1kimA 366 -31.63 -6.80 3.68e+01 1kp9B 287 -30.95 -6.79 3.72e+01 1g0rA 293 -29.34 -6.78 3.73e+01 1qhiA 366 -31.63 -6.78 3.73e+01 1c3oA 1073 -34.01 -6.78 3.74e+01 1eguA 731 -37.98 -6.73 3.85e+01 1eh9A 558 -32.83 -6.72 3.85e+01 1ekxA 311 -29.44 -6.70 3.91e+01