% 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. % --------------------------------------------------------------------- % alphafoo.1.YDR031W.t2k-100-30-alpha Host: farm12.cse.ucsc.edu Fri Mar 3 08:29:12 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.alphas % % 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.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14381 sequences, 3373755 residues, 122 nodes, 204.46 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(=3.2781) * Reverse)^tau(=0.6780))) % 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 1xg5A 279 -16.03 -7.19 2.19e+00 1jqaA 370 -14.94 -6.85 2.89e+00 1jq5A 370 -14.93 -6.84 2.92e+00 1p8cA 145 -16.07 -6.83 2.94e+00 1vkeA 133 -15.85 -6.55 3.68e+00 1hg4A 279 -18.34 -6.36 4.34e+00 1fpzA 212 -15.84 -6.24 4.79e+00 1e85A 127 -15.72 -6.22 4.86e+00 1jkgB 250 -14.55 -6.20 4.94e+00 1mznA 240 -16.18 -6.00 5.84e+00 1cgo 127 -15.35 -5.97 6.01e+00 1jn5B 250 -14.06 -5.73 7.40e+00 1q4mA 221 -18.16 -5.72 7.45e+00 1mc2A 122 -15.47 -5.69 7.65e+00 1ow5A 85 -15.00 -5.67 7.80e+00 1xiuA 230 -14.90 -5.63 8.03e+00 1pc6A 146 -13.93 -5.57 8.48e+00 1mvcA 240 -16.17 -5.48 9.19e+00 1ci0A 228 -13.19 -5.42 9.67e+00 1zs9A 261 -14.63 -5.40 9.85e+00 1poc 134 -13.81 -5.32 1.06e+01 2f2gA 221 -17.70 -5.28 1.10e+01 1tq4A 413 -13.88 -5.21 1.16e+01 1q3iA 214 -14.02 -5.11 1.27e+01 1c3cA 429 -15.20 -4.94 1.49e+01 1vf1A 229 -13.13 -4.93 1.50e+01 1g3gA 164 -12.35 -4.92 1.52e+01 3ygsP 97 -13.15 -4.91 1.53e+01 2a19A 175 -12.95 -4.90 1.54e+01 1ie9A 259 -14.72 -4.86 1.60e+01 1dkfA 233 -15.09 -4.74 1.78e+01 1fm0D 81 -11.64 -4.73 1.80e+01 1ta9A 450 -13.38 -4.72 1.82e+01 1gk8I 140 -12.20 -4.72 1.82e+01 1v74A 107 -12.05 -4.70 1.85e+01 1ju2A 536 -13.15 -4.68 1.89e+01 1kq3A 376 -13.46 -4.68 1.89e+01 1fmaD 81 -11.53 -4.62 1.99e+01 1i37A 260 -14.39 -4.57 2.09e+01 2cro 71 -11.76 -4.55 2.13e+01 1e0bA 68 -13.02 -4.52 2.18e+01 1z3iX 644 -14.29 -4.51 2.20e+01 1naqA 112 -12.41 -4.47 2.28e+01 1kq4A 232 -13.82 -4.42 2.39e+01 1ir21 140 -11.81 -4.42 2.40e+01 1ppa 121 -14.24 -4.41 2.42e+01 1o26A 232 -13.89 -4.40 2.44e+01 1go5A 69 -12.39 -4.39 2.46e+01 1ixkA 315 -13.00 -4.37 2.51e+01 1djxA 624 -12.90 -4.37 2.51e+01 1oaiA 59 -13.13 -4.24 2.85e+01 2a9uA 144 -13.14 -4.23 2.87e+01 1obr 326 -12.22 -4.23 2.88e+01 1q1lA 401 -12.78 -4.23 2.88e+01 1g5yA 238 -14.40 -4.21 2.93e+01 1mba 147 -13.01 -4.19 2.99e+01 1rz4A 226 -12.96 -4.17 3.03e+01 1jjfA 268 -12.39 -4.17 3.03e+01 2fal 147 -12.90 -4.10 3.26e+01 1iyhA 198 -12.82 -4.10 3.26e+01 1y8qA 346 -12.91 -4.08 3.32e+01 1vl6A 388 -12.52 -4.04 3.46e+01 1jxcA 68 -12.21 -4.03 3.47e+01 1e6yA 569 -12.96 -4.03 3.48e+01 1i39A 225 -12.54 -4.03 3.48e+01 1is1A 185 -13.21 -3.99 3.63e+01 1rwtA 232 -13.12 -3.94 3.78e+01 1s8iA 121 -13.73 -3.93 3.84e+01 1xo5A 183 -13.12 -3.93 3.84e+01 1db1A 259 -14.40 -3.91 3.89e+01 1ti6B 274 -11.46 -3.91 3.92e+01 1wn5A 130 -11.74 -3.90 3.96e+01 1cb2A 365 -14.23 -3.89 3.99e+01 1djxB 624 -12.29 -3.89 4.00e+01