% 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.YGR212W.t2k-100-30-dssp-ebghstl Host: cc50 Sun Oct 12 00:49:21 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR212W % --------------------------------------------------------------------- % 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 YGR212W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR212W.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8763 sequences, 2072585 residues, 469 nodes, 439.78 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(=1.4982) * Reverse)^tau(=0.7752))) % 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 1l5aA 436 -38.82 -14.64 1.43e-01 1i19A 561 -34.75 -10.32 1.92e+00 1bgp 309 -32.08 -9.35 3.55e+00 8pchA 220 -30.50 -8.90 4.74e+00 1h2aL 567 -32.74 -8.29 7.05e+00 1dmuA 299 -32.21 -8.26 7.22e+00 1oe4A 247 -31.68 -8.25 7.28e+00 8acn 754 -33.82 -8.20 7.49e+00 1a15A 67 -27.39 -8.18 7.62e+00 1amj 754 -33.82 -8.14 7.82e+00 1gskA 513 -32.94 -7.97 8.75e+00 1lnsA 763 -33.69 -7.90 9.13e+00 1azo 232 -30.04 -7.70 1.04e+01 1el6A 219 -30.54 -7.56 1.15e+01 1el6B 219 -30.61 -7.53 1.17e+01 1g4uS 383 -33.81 -7.50 1.20e+01 1keiA 316 -30.71 -7.43 1.25e+01 1b0jA 754 -33.32 -7.40 1.29e+01 1gqeA 365 -31.44 -7.38 1.30e+01 1qg7A 67 -27.22 -7.33 1.34e+01 1gnlA 544 -31.07 -7.25 1.42e+01 2tmnE 316 -30.51 -7.21 1.46e+01 7acn 754 -33.40 -7.18 1.49e+01 6tmnE 316 -30.51 -7.18 1.49e+01 1c96A 753 -33.41 -7.18 1.49e+01 8tlnE 316 -30.51 -7.17 1.49e+01 1hyt 316 -30.51 -7.17 1.49e+01 1g4wR 383 -33.32 -7.13 1.54e+01 6acn 754 -33.36 -7.11 1.56e+01 1e3dB 542 -31.16 -7.09 1.58e+01 1fljA 260 -30.13 -6.99 1.69e+01 1eaxA 241 -30.11 -6.96 1.73e+01 1cxqA 162 -28.54 -6.91 1.79e+01 1f5mB 180 -29.75 -6.88 1.82e+01 1f5mA 180 -29.77 -6.87 1.83e+01 1jvpP 298 -31.96 -6.86 1.86e+01 1h3gA 601 -32.00 -6.82 1.90e+01 1mkiA 330 -30.59 -6.80 1.93e+01 1vsd 152 -28.35 -6.71 2.05e+01 1gwuA 309 -29.29 -6.60 2.21e+01 1ayx 492 -31.08 -6.58 2.24e+01 1gk8A 475 -31.00 -6.56 2.28e+01 1k6iA 352 -30.69 -6.50 2.37e+01 1gsoA 431 -30.65 -6.50 2.37e+01 2atjA 308 -29.11 -6.49 2.38e+01 1k94A 165 -28.25 -6.49 2.40e+01 7atjA 308 -29.06 -6.46 2.43e+01 1ubkL 534 -32.42 -6.45 2.46e+01 1hcl 298 -31.42 -6.43 2.49e+01 1k6xA 352 -30.63 -6.41 2.52e+01 1o7fA 469 -29.59 -6.39 2.57e+01 1m1nB 522 -31.14 -6.37 2.60e+01 1l1lA 739 -31.52 -6.34 2.66e+01 1mwsA 646 -31.40 -6.33 2.67e+01 1parA 53 -25.02 -6.31 2.71e+01 1asu 162 -28.56 -6.31 2.71e+01 1bk1 184 -28.09 -6.31 2.72e+01 1uc8A 280 -28.57 -6.31 2.72e+01 1l8fA 207 -30.10 -6.30 2.73e+01 1f4qA 165 -27.45 -6.25 2.82e+01 1jhnA 424 -31.21 -6.20 2.91e+01 1gz8A 299 -31.09 -6.19 2.94e+01 1fzvA 132 -27.79 -6.19 2.94e+01 1bxvA 91 -26.09 -6.18 2.96e+01 2minB 522 -30.65 -6.13 3.08e+01 3minB 522 -30.88 -6.08 3.17e+01 1bdtA 53 -24.71 -6.06 3.24e+01 1jkgA 140 -27.50 -6.05 3.26e+01 1e1xA 299 -31.08 -6.03 3.29e+01 1h2rL 534 -32.19 -5.99 3.38e+01 1ayyA 151 -26.67 -5.91 3.58e+01 1mwxA 646 -30.87 -5.85 3.74e+01 1suh 146 -27.81 -5.79 3.90e+01