% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (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.T0242.t04-100-30-bys Host: chirp Thu Aug 12 09:31:20 2004 % sol Dir: /projects/compbio/experiments/protein-predict/casp6/T0242 % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t04.x-seqs,/projects/compbio/experiments/models.97/indexes/t04.byss % % 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 T0242.t04.w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File T0242.t04.bys.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 6749 sequences, 1593535 residues, 117 nodes, 30.36 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 (0.00) % E-value on N (=10183) sequences: % N / (1 + exp(-(lambda(=2.6846) * Reverse)^tau(=0.6674))) % 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 1uu1A 335 -19.40 -10.77 8.06e-01 1b9wA 89 -15.27 -7.87 4.81e+00 1gmuA 143 -15.76 -7.45 6.32e+00 1n3yA 198 -16.20 -7.31 6.95e+00 1fxlA 167 -15.26 -7.17 7.60e+00 1izcA 339 -16.37 -7.04 8.32e+00 1vkmA 297 -15.19 -6.95 8.85e+00 1pyoA 167 -14.53 -6.39 1.30e+01 1bjwA 382 -14.48 -6.34 1.35e+01 1fs7A 485 -14.41 -6.23 1.45e+01 1gwiA 411 -14.04 -6.17 1.51e+01 1rypA 243 -14.62 -5.96 1.76e+01 1f7dA 136 -13.83 -5.94 1.78e+01 1iw7C 1119 -14.43 -5.83 1.93e+01 1kq3A 376 -14.28 -5.72 2.08e+01 1b5pA 385 -13.79 -5.69 2.13e+01 1dgyA 363 -14.24 -5.68 2.14e+01 1liiA 363 -14.24 -5.67 2.15e+01 1g6aA 271 -13.48 -5.64 2.20e+01 1gs5A 258 -15.18 -5.63 2.22e+01 1jbkA 195 -13.93 -5.58 2.30e+01 1id0A 152 -14.70 -5.54 2.37e+01 1kgdA 180 -14.19 -5.44 2.55e+01 1nmoA 247 -13.77 -5.43 2.58e+01 1rhs 296 -13.14 -5.25 2.94e+01 1g6hA 257 -15.14 -5.21 3.01e+01 1h9mA 145 -13.83 -5.16 3.13e+01 1ir6A 424 -13.20 -5.16 3.13e+01 1iyhA 198 -13.98 -5.10 3.28e+01 1jwiA 131 -12.33 -5.05 3.40e+01 1lci 550 -13.72 -5.01 3.51e+01 1v5xA 203 -12.69 -4.99 3.58e+01 1vicA 262 -13.94 -4.98 3.60e+01 1bb9 115 -12.90 -4.96 3.65e+01 1lhpA 312 -13.50 -4.88 3.89e+01 1ituA 369 -12.82 -4.87 3.89e+01 1pd21 199 -13.48 -4.87 3.90e+01 1o0wA 252 -13.72 -4.86 3.94e+01 1n57A 291 -12.54 -4.86 3.94e+01