% 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. % --------------------------------------------------------------------- % stridefoo.1.YGR023W.t2k-100-30-stride-ebghtl Host: farm19.cse.ucsc.edu Sun Mar 19 11:58:10 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR023W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.2ds % % 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 YGR023W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR023W.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14489 sequences, 3401351 residues, 552 nodes, 915.74 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(=1.2377) * Reverse)^tau(=0.8194))) % 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 1jk7A 323 -26.55 -13.12 6.01e-01 1u32A 293 -25.72 -12.94 6.69e-01 1fjmA 330 -26.17 -12.63 8.10e-01 1d0nA 729 -27.08 -11.30 1.86e+00 1gqpA 221 -26.33 -10.94 2.33e+00 1f28A 297 -22.81 -10.11 3.96e+00 1zckA 154 -22.91 -9.98 4.30e+00 1ziwA 680 -31.82 -9.67 5.25e+00 1rxdA 159 -22.60 -9.60 5.51e+00 1wkrA 340 -34.95 -9.56 5.66e+00 1p8xA 344 -24.27 -9.51 5.84e+00 1adqH 225 -33.38 -9.44 6.11e+00 2bzlA 325 -25.22 -9.03 8.00e+00 1z41A 338 -20.12 -8.89 8.74e+00 1q40B 219 -23.82 -8.83 9.08e+00 1d8dB 437 -20.54 -8.80 9.26e+00 1rmg 422 -32.93 -8.72 9.77e+00 1eysH 259 -28.86 -8.67 1.01e+01 1prcH 259 -28.05 -8.66 1.02e+01 1mkfA 382 -30.27 -8.50 1.13e+01 1tdtA 259 -24.80 -8.40 1.21e+01 6prcH 258 -28.23 -8.33 1.27e+01 1kgqA 274 -24.22 -8.21 1.37e+01 1jcrB 437 -19.86 -8.07 1.51e+01 1dxrH 258 -28.02 -8.04 1.54e+01 1wguA 136 -21.84 -7.99 1.59e+01 1cjtA 217 -18.89 -7.98 1.60e+01 1dxrL 273 -22.61 -7.98 1.60e+01 1yzfA 195 -20.24 -7.98 1.60e+01 1l6rA 227 -18.86 -7.96 1.63e+01 1azsA 220 -19.06 -7.93 1.66e+01 1p30A 952 -29.02 -7.91 1.68e+01 1bqhG 129 -27.36 -7.88 1.71e+01 1t5hX 504 -24.97 -7.86 1.73e+01 1bt3A 345 -22.64 -7.83 1.77e+01 1upiA 225 -28.58 -7.83 1.77e+01 1e2tA 284 -22.85 -7.83 1.78e+01 1avk 638 -28.70 -7.82 1.78e+01 6prcL 273 -22.64 -7.80 1.81e+01 1eaf 243 -20.47 -7.78 1.83e+01 2bvyA 475 -24.15 -7.75 1.87e+01 1k42A 168 -27.00 -7.65 2.01e+01 1ft1B 437 -19.35 -7.58 2.10e+01 1dpb 243 -20.25 -7.53 2.16e+01 1try 224 -33.14 -7.49 2.23e+01 1o0uA 429 -18.95 -7.48 2.24e+01 1culA 217 -18.23 -7.46 2.27e+01 1pujA 282 -19.21 -7.40 2.36e+01 1itkA 731 -22.06 -7.40 2.37e+01 1uteA 313 -22.92 -7.38 2.39e+01 2tdt 274 -23.03 -7.38 2.40e+01 2sqcA 631 -19.14 -7.38 2.41e+01 3tdt 274 -23.04 -7.36 2.43e+01 2b8nA 429 -18.54 -7.36 2.44e+01 1pq7A 224 -32.97 -7.32 2.50e+01 1fn8A 224 -32.93 -7.29 2.55e+01 1air 353 -28.55 -7.26 2.61e+01 2pec 353 -28.55 -7.26 2.61e+01 1sqc 631 -19.07 -7.23 2.66e+01 2aaiB 262 -31.14 -7.17 2.77e+01 1xszA 356 -18.13 -7.17 2.77e+01 1qfcA 306 -22.03 -7.15 2.81e+01 1z3iX 644 -20.83 -7.14 2.82e+01 1z90A 469 -20.48 -7.13 2.85e+01 1zpsA 138 -21.27 -7.03 3.05e+01 1a5fH 217 -31.21 -7.00 3.10e+01 2fcr 173 -21.29 -7.00 3.12e+01 2cvhA 220 -18.82 -6.99 3.12e+01 1ai1H 221 -37.53 -6.99 3.13e+01 2bbkH 355 -28.56 -6.99 3.13e+01 1npeA 267 -28.45 -6.98 3.15e+01 1j0fA 100 -16.98 -6.98 3.16e+01 1wyuA 438 -20.34 -6.94 3.25e+01 2rmpA 361 -32.90 -6.93 3.26e+01 1m2tB 263 -30.06 -6.93 3.27e+01 1ktbA 405 -25.10 -6.88 3.38e+01 1ae6H 218 -32.16 -6.85 3.44e+01 1tn6B 437 -18.98 -6.84 3.46e+01 1ar1B 298 -23.35 -6.84 3.47e+01 1q9jA 422 -20.78 -6.78 3.61e+01 1ollA 188 -25.32 -6.75 3.68e+01 1qh4A 380 -20.03 -6.75 3.69e+01 1ld8B 437 -18.79 -6.71 3.80e+01 1o88A 353 -27.95 -6.67 3.90e+01