% 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. % --------------------------------------------------------------------- % str2foo.1.YGR213C.t2k-100-30-str2 Host: farm01 Wed Dec 1 18:19:17 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.str2s % % 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.str2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10944 sequences, 2597075 residues, 318 nodes, 340.60 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 (0.00) % E-value on N (=10700) sequences: % N / (1 + exp(-(lambda(=2.0349) * Reverse)^tau(=0.7660))) % 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 1fqyA 269 -27.63 -11.62 1.35e-01 1j4nA 271 -32.01 -11.20 1.85e-01 1dxrH 258 -22.99 -10.74 2.62e-01 6prcH 258 -22.86 -10.61 2.89e-01 1jalA 363 -20.48 -9.57 6.40e-01 1tlqA 189 -21.79 -9.37 7.49e-01 1i37A 260 -21.44 -8.47 1.53e+00 1t7rA 269 -21.30 -8.02 2.19e+00 1jb0A 755 -29.18 -7.85 2.52e+00 1e2xA 243 -21.58 -7.82 2.58e+00 1ayx 492 -21.78 -7.81 2.61e+00 1ih7A 903 -21.20 -7.79 2.66e+00 1oshA 232 -22.22 -7.75 2.74e+00 1hw1A 239 -21.68 -7.47 3.43e+00 1clqA 903 -20.38 -7.03 4.97e+00 1aoa 275 -20.76 -6.99 5.13e+00 1dofA 403 -21.11 -6.94 5.37e+00 1mjgM 729 -20.94 -6.86 5.71e+00 1nyhA 166 -22.20 -6.84 5.82e+00 1be3C 379 -28.26 -6.78 6.10e+00 1a8h 500 -18.89 -6.72 6.46e+00 1oaoC 729 -20.59 -6.57 7.34e+00 1pl5A 142 -22.22 -6.53 7.56e+00 1oa4A 222 -15.65 -6.43 8.27e+00 1hz4A 373 -18.45 -6.37 8.64e+00 2hmx 133 -19.95 -6.20 1.01e+01 1v54A 514 -29.83 -6.14 1.06e+01 1vkeA 133 -17.10 -6.13 1.07e+01 2occA 514 -29.31 -5.98 1.22e+01 1dxrM 323 -21.71 -5.91 1.29e+01 1omwA 689 -18.19 -5.85 1.36e+01 1qlaC 256 -27.08 -5.63 1.65e+01 1gkzA 388 -20.20 -5.61 1.68e+01 1p8cA 145 -16.41 -5.59 1.71e+01 1qv9A 283 -19.80 -5.56 1.75e+01 1d7mA 101 -17.18 -5.35 2.11e+01 1wer 334 -18.92 -5.29 2.23e+01 1iomA 377 -18.27 -5.26 2.28e+01 1fp1D 372 -16.49 -5.23 2.35e+01 1ehkA 562 -26.94 -5.22 2.37e+01 1up8A 598 -17.74 -5.22 2.37e+01 1xc0A 33 -14.09 -5.20 2.42e+01 1jmeA 455 -21.32 -5.08 2.70e+01 1gkxA 388 -20.43 -5.01 2.85e+01 1gk4C 84 -19.31 -5.01 2.87e+01 1sqnA 261 -19.27 -4.96 2.99e+01 1sr7A 259 -19.27 -4.96 2.99e+01 1ifa 158 -17.23 -4.94 3.05e+01 1jpzA 473 -20.31 -4.91 3.12e+01 6prcM 323 -21.17 -4.90 3.17e+01 1gk4A 84 -18.49 -4.85 3.31e+01 1ithA 141 -16.70 -4.84 3.35e+01 1ks9A 291 -17.40 -4.82 3.39e+01 1noyA 388 -17.61 -4.79 3.48e+01 1jotA 133 -13.50 -4.79 3.50e+01 1ireB 228 -16.94 -4.78 3.54e+01 1upvA 257 -20.63 -4.77 3.56e+01 1f1oA 431 -18.55 -4.75 3.61e+01 1ugpB 226 -16.93 -4.75 3.62e+01 1uynX 308 -13.92 -4.74 3.67e+01 1914 232 -14.94 -4.73 3.69e+01 1gk4D 84 -18.41 -4.72 3.74e+01 1k0fA 277 -15.21 -4.71 3.77e+01 1edoA 244 -16.28 -4.69 3.83e+01 1riqA 465 -20.27 -4.69 3.84e+01 1eysH 259 -17.11 -4.68 3.85e+01 1a28A 256 -19.14 -4.65 3.97e+01