% 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. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YDR031W.t2k-100-30-dssp-ehl2 Host: farm12.cse.ucsc.edu Fri Mar 3 08:36:26 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YDR0/YDR031W % --------------------------------------------------------------------- % 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 +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YDR031W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YDR031W.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14381 sequences, 3373755 residues, 122 nodes, 204.60 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(=2.6325) * Reverse)^tau(=0.7036))) % 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 1hg4A 279 -20.74 -8.20 1.87e+00 1ow5A 85 -18.18 -7.97 2.22e+00 1jq5A 370 -16.61 -7.84 2.44e+00 1jqaA 370 -16.61 -7.83 2.46e+00 1q3iA 214 -17.33 -7.02 4.58e+00 1vkeA 133 -17.25 -6.59 6.43e+00 1mc2A 122 -17.21 -6.55 6.61e+00 1q4mA 221 -19.85 -6.39 7.53e+00 1dguA 183 -16.95 -6.35 7.76e+00 1ta9A 450 -16.23 -6.25 8.44e+00 1p8cA 145 -16.63 -6.12 9.34e+00 1ie9A 259 -17.91 -6.10 9.48e+00 1z3iX 644 -17.17 -6.01 1.02e+01 2f2gA 221 -19.22 -6.01 1.03e+01 1rz4A 226 -16.58 -5.98 1.05e+01 1xiuA 230 -16.21 -5.97 1.06e+01 1v74A 107 -13.87 -5.91 1.11e+01 1e85A 127 -15.94 -5.82 1.20e+01 1xwmA 217 -16.93 -5.79 1.22e+01 1mznA 240 -17.41 -5.78 1.23e+01 1ju2A 536 -14.93 -5.77 1.24e+01 1vf1A 229 -14.76 -5.77 1.25e+01 1cgo 127 -15.94 -5.74 1.27e+01 1zs9A 261 -16.33 -5.73 1.29e+01 2a19A 175 -14.32 -5.64 1.39e+01 1pc6A 146 -14.77 -5.60 1.43e+01 1htjF 210 -15.12 -5.58 1.46e+01 1fpzA 212 -16.25 -5.54 1.50e+01 1z0xA 220 -14.91 -5.44 1.64e+01 1mvcA 240 -17.37 -5.40 1.69e+01 1xg5A 279 -15.78 -5.36 1.75e+01 1ir21 140 -13.11 -5.35 1.77e+01 1gk8I 140 -13.10 -5.34 1.78e+01 1jkgB 250 -13.88 -5.31 1.83e+01 1ci0A 228 -13.51 -5.30 1.85e+01 2cro 71 -12.91 -5.28 1.87e+01 1kx9A 112 -16.13 -5.16 2.09e+01 1naqA 112 -13.02 -5.12 2.15e+01 1kq3A 376 -14.86 -5.10 2.19e+01 2bbvA 363 -13.09 -5.08 2.22e+01 1mtyB 384 -14.37 -5.01 2.37e+01 1jn5B 250 -13.56 -5.01 2.37e+01 1mmoB 384 -14.37 -5.01 2.37e+01 1f8vA 355 -12.59 -4.91 2.59e+01 1g5yA 238 -16.43 -4.90 2.59e+01 1w1kA 560 -14.10 -4.84 2.74e+01 1g3gA 164 -12.84 -4.82 2.79e+01 1e8gA 560 -14.17 -4.82 2.80e+01 1q1lA 401 -13.75 -4.81 2.82e+01 1tq4A 413 -14.01 -4.80 2.85e+01 1qltA 560 -14.10 -4.79 2.86e+01 1n1fA 159 -15.96 -4.79 2.87e+01 1eysL 280 -15.40 -4.74 2.99e+01 2bbvC 363 -12.54 -4.70 3.10e+01 1cb2A 365 -15.37 -4.69 3.11e+01 2a9uA 144 -14.21 -4.67 3.17e+01 1t6nA 220 -13.95 -4.62 3.32e+01 3ygsP 97 -13.33 -4.61 3.35e+01 1gotG 73 -15.78 -4.59 3.40e+01 1zug 71 -12.17 -4.55 3.54e+01 1djxA 624 -13.43 -4.54 3.58e+01 1twfB 1224 -14.24 -4.53 3.59e+01 1e6yA 569 -13.88 -4.51 3.67e+01 1a0rG 65 -15.60 -4.48 3.77e+01 1qatB 622 -13.30 -4.47 3.78e+01 1rwtA 232 -14.47 -4.44 3.88e+01 1ib8A 164 -12.62 -4.44 3.91e+01 1lbd 282 -15.98 -4.43 3.93e+01