% 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. % --------------------------------------------------------------------- % stridefoo.1.YGR213C.t2k-100-30-stride-ebghtl Host: farm01 Wed Dec 1 18:42:02 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR213C % --------------------------------------------------------------------- % 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 YGR213C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR213C.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10944 sequences, 2597075 residues, 318 nodes, 339.82 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 (=10700) sequences: % N / (1 + exp(-(lambda(=1.9738) * Reverse)^tau(=0.7279))) % 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 1tlqA 189 -25.61 -10.48 1.23e+00 1ks9A 291 -22.15 -9.55 2.23e+00 1ithA 141 -22.59 -9.54 2.24e+00 1vmgA 95 -23.76 -9.13 2.92e+00 1q0gA 117 -19.92 -8.22 5.35e+00 1t56A 216 -22.65 -8.16 5.56e+00 1toaA 313 -18.97 -8.13 5.67e+00 1i37A 260 -22.04 -7.98 6.28e+00 1swxA 209 -22.79 -7.87 6.79e+00 1t7rA 269 -21.64 -7.78 7.20e+00 1g8iA 190 -20.51 -7.59 8.19e+00 1p8cA 145 -19.33 -7.53 8.57e+00 1dxrH 258 -21.74 -7.52 8.59e+00 1j4nA 271 -29.56 -7.27 1.02e+01 1jalA 363 -20.23 -7.26 1.03e+01 1dt6A 473 -20.77 -7.24 1.04e+01 1ih7A 903 -21.28 -7.18 1.09e+01 6prcH 258 -21.34 -7.16 1.10e+01 1h7eA 245 -17.94 -7.13 1.13e+01 1vkeA 133 -18.98 -7.07 1.17e+01 1iomA 377 -20.05 -6.99 1.24e+01 1jb0A 755 -32.26 -6.99 1.25e+01 1eia 207 -19.42 -6.90 1.33e+01 1fggA 261 -16.63 -6.90 1.33e+01 1kwsA 261 -16.63 -6.89 1.33e+01 1gkmA 509 -22.52 -6.86 1.37e+01 1lw3A 657 -19.43 -6.74 1.48e+01 1ll7A 392 -19.50 -6.70 1.53e+01 1eagA 342 -15.92 -6.66 1.57e+01 1b8fA 509 -21.76 -6.66 1.57e+01 1dofA 403 -22.96 -6.66 1.57e+01 2eiaB 206 -19.45 -6.65 1.58e+01 1d2kA 392 -20.02 -6.57 1.68e+01 1tk1A 260 -20.79 -6.50 1.77e+01 1oshA 232 -22.10 -6.47 1.81e+01 1qgrA 876 -28.06 -6.46 1.82e+01 1n6bA 473 -19.89 -6.40 1.89e+01 1k0fA 277 -16.76 -6.34 1.97e+01 1rzhL 281 -26.52 -6.25 2.11e+01 1nzeA 149 -20.41 -6.20 2.18e+01 1rzhM 307 -24.56 -6.16 2.25e+01 1qv9A 283 -22.18 -6.09 2.37e+01 1clqA 903 -20.02 -6.04 2.46e+01 1fqyA 269 -24.32 -5.99 2.54e+01 1nr6A 473 -19.24 -5.96 2.61e+01 1pl5A 142 -21.23 -5.86 2.80e+01 1etu 394 -19.42 -5.82 2.89e+01 1e9xA 455 -19.65 -5.76 3.03e+01 1eysH 259 -18.39 -5.73 3.08e+01 1io7A 368 -19.04 -5.67 3.24e+01 1ovlA 271 -22.05 -5.65 3.27e+01 1gqeA 365 -18.46 -5.61 3.37e+01 1pszA 303 -18.70 -5.60 3.40e+01 1dxrM 323 -22.30 -5.54 3.54e+01 1nyhA 166 -20.92 -5.53 3.59e+01 1jfmA 174 -17.00 -5.52 3.60e+01 1iakA 199 -15.25 -5.52 3.61e+01 1pt7A 437 -17.09 -5.48 3.71e+01 6prcM 323 -23.17 -5.47 3.74e+01 1yveJ 524 -23.04 -5.45 3.81e+01 1q7eA 428 -17.06 -5.42 3.89e+01