% 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. % --------------------------------------------------------------------- % CB_burial_14_7foo.1.YGR213C.t2k-100-40-40-str2+CB_burial_14_7 Host: farm01 Wed Dec 1 19:16:52 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,/projects/compbio/experiments/models.97/indexes/t2k.CB-burial-14-7s % % 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 0.400 File YGR213C.t2k.str2.mod % Track 2 FIMs added (the generic node (5)) % Track 2 Coeff 0.400 File YGR213C.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10944 sequences, 2597075 residues, 318 nodes, 380.71 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(=1.0287) * Reverse)^tau(=0.7667))) % 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 1jmeA 455 -50.84 -27.28 2.70e-02 6prcM 323 -43.02 -20.09 3.99e-01 2bmhA 455 -49.26 -19.92 4.27e-01 1dxrM 323 -44.05 -19.38 5.26e-01 1bu7A 455 -46.94 -19.11 5.87e-01 1a7aA 432 -33.67 -18.77 6.70e-01 1jpzA 473 -47.42 -18.66 7.01e-01 2pgd 482 -43.57 -17.90 9.49e-01 1li4A 432 -30.91 -16.50 1.66e+00 1j7nA 776 -33.10 -15.88 2.15e+00 1b3rA 431 -29.72 -15.31 2.72e+00 1oaoC 729 -34.15 -15.30 2.73e+00 1d4fA 431 -30.02 -14.80 3.37e+00 1jb0A 755 -43.92 -14.41 3.96e+00 1i6iA 366 -29.15 -14.23 4.26e+00 1mjgM 729 -33.00 -13.94 4.83e+00 1aoa 275 -35.72 -13.83 5.06e+00 1j93A 353 -27.59 -13.74 5.26e+00 1qo7A 394 -31.28 -13.44 5.97e+00 1vfvA 366 -27.82 -13.33 6.26e+00 1uynX 308 -23.99 -13.27 6.41e+00 1i5sA 367 -27.73 -13.25 6.47e+00 2hmx 133 -34.65 -12.74 8.06e+00 1h21A 247 -32.81 -12.46 9.11e+00 1aroP 883 -32.15 -12.42 9.26e+00 1q41A 424 -26.79 -12.38 9.44e+00 6prcH 258 -37.50 -12.37 9.46e+00 1dxrH 258 -37.42 -12.27 9.87e+00 1ca1 370 -27.90 -12.19 1.02e+01 1q5nA 454 -29.79 -11.99 1.12e+01 1ddcA 247 -27.91 -11.83 1.20e+01 1j1bA 420 -27.76 -11.76 1.24e+01 1h38D 883 -33.82 -11.09 1.67e+01 1t7pA 698 -33.20 -11.09 1.67e+01 1fqyA 269 -33.91 -11.05 1.69e+01 1wer 334 -34.31 -11.00 1.73e+01 1b8fA 509 -30.01 -10.89 1.82e+01 1h38B 883 -32.89 -10.84 1.86e+01 1fi4A 416 -26.70 -10.81 1.89e+01 1kmnD 424 -25.51 -10.74 1.94e+01 1tlqA 189 -30.58 -10.74 1.95e+01 1h38C 883 -32.82 -10.73 1.96e+01 1iznB 277 -31.48 -10.70 1.98e+01 1dkqA 410 -29.44 -10.63 2.05e+01 1j7nB 776 -28.42 -10.56 2.11e+01 1gxyA 226 -26.35 -10.47 2.19e+01 1yts 278 -28.03 -10.46 2.20e+01 1dkmA 410 -29.87 -10.45 2.22e+01 1f74A 293 -24.17 -10.44 2.22e+01 3vtk 343 -26.09 -10.36 2.31e+01 1f6kA 293 -23.89 -10.33 2.34e+01 1odoA 408 -27.75 -10.23 2.45e+01 1yptA 305 -28.22 -10.19 2.49e+01 1f24A 402 -30.74 -10.07 2.63e+01 1ukvG 453 -29.28 -10.05 2.65e+01 1l4sA 112 -29.81 -10.00 2.72e+01 1ei6A 406 -20.78 -10.00 2.72e+01 1itzA 675 -27.01 -9.96 2.77e+01 1ytw 306 -29.08 -9.90 2.85e+01 1jkvA 266 -32.22 -9.87 2.88e+01 4xiaA 393 -29.64 -9.81 2.97e+01 1x9mA 698 -30.67 -9.75 3.05e+01 1gkmA 509 -29.16 -9.69 3.14e+01 1cmnA 402 -29.17 -9.60 3.26e+01 2lbd 267 -30.02 -9.39 3.60e+01 1vkhA 273 -23.05 -9.36 3.65e+01 1o9iA 266 -31.50 -9.22 3.89e+01 5eat 548 -28.50 -9.22 3.90e+01 1bgc 174 -26.05 -9.20 3.93e+01 1pot 325 -23.07 -9.19 3.96e+01