% SAM: /projects/compbio/bin/i686/hmmscore v3.3.2 (February, 2001) compiled 06/24/02_10:50:12 % (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-T99, 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, C. Barrett, R. Hughey, Hidden Markov models for detecting % remote protein homologies, Bioinformatics 14(10):846-856, 1998. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % alphafoo.1.YGR213C.t2k-100-30-alpha Host: cc65 Tue Nov 12 16:31:41 2002 % 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.alphas % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by 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.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 318 nodes, 227.99 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 (=7316) sequences: % N / (1 + exp(-(lambda(=3.1033) * Reverse)^tau(=0.7205))) % 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 1jb0A 755 -39.97 -11.24 1.79e-02 6prcH 258 -30.47 -8.48 1.92e-01 1dxrH 258 -29.84 -7.84 3.41e-01 1i37A 260 -28.83 -6.65 1.04e+00 1aoa 275 -29.47 -6.18 1.65e+00 1d2kA 392 -28.56 -6.10 1.78e+00 1fp1D 372 -27.96 -5.71 2.63e+00 1clqA 903 -30.01 -5.52 3.17e+00 1i50B 1224 -31.37 -5.52 3.18e+00 4lbd 267 -30.11 -5.48 3.31e+00 1g8iA 190 -26.74 -5.33 3.86e+00 1hw1A 239 -27.72 -5.21 4.34e+00 1eysH 259 -27.73 -5.17 4.51e+00 1b8fA 509 -29.59 -5.14 4.65e+00 2lbd 267 -29.77 -5.00 5.42e+00 1qgrA 876 -33.15 -4.98 5.50e+00 1fcyA 236 -29.21 -4.91 5.90e+00 2occA 514 -34.52 -4.88 6.10e+00 1dxrM 323 -29.03 -4.79 6.75e+00 2aat 396 -26.15 -4.78 6.79e+00 1ks9A 291 -26.96 -4.72 7.25e+00 1ytfD 121 -23.66 -4.67 7.67e+00 1fqyA 269 -28.38 -4.65 7.82e+00 1jb0L 154 -30.19 -4.59 8.31e+00 6prcM 323 -28.92 -4.55 8.66e+00 1elt 236 -25.06 -4.49 9.20e+00 1fpqA 372 -26.64 -4.39 1.03e+01 2sfa 191 -23.90 -4.36 1.06e+01 1ithA 141 -25.61 -4.34 1.09e+01 1gkmA 509 -28.71 -4.30 1.13e+01 1dofA 403 -28.54 -4.26 1.18e+01 1e2xA 243 -26.71 -4.18 1.29e+01 1dt6A 473 -27.38 -4.07 1.45e+01 1ars 396 -25.76 -4.05 1.49e+01 1dkgB 197 -25.83 -4.05 1.50e+01 1qisA 396 -25.80 -4.02 1.54e+01 1gh2A 107 -22.20 -4.01 1.55e+01 1fkmA 396 -31.56 -4.01 1.56e+01 1spa 396 -25.79 -4.00 1.57e+01 1art 396 -25.71 -3.93 1.70e+01 1ireB 228 -25.05 -3.92 1.72e+01 1qkkA 155 -23.32 -3.85 1.85e+01 1ahxA 396 -25.45 -3.79 1.99e+01 2u1a 88 -21.34 -3.77 2.03e+01 1ajqA 209 -24.09 -3.72 2.16e+01 1ibcA 194 -23.63 -3.69 2.23e+01 1brd 248 -36.37 -3.68 2.24e+01 1qlaC 256 -30.16 -3.66 2.30e+01 1pnkA 209 -23.98 -3.65 2.31e+01 1mkaA 171 -23.54 -3.61 2.43e+01 1kwsA 261 -24.01 -3.59 2.48e+01 1eciB 34 -19.21 -3.53 2.65e+01 16vpA 366 -27.70 -3.51 2.73e+01 1e8oA 85 -22.42 -3.50 2.75e+01 1fggA 261 -23.91 -3.50 2.77e+01 2at9 247 -28.48 -3.49 2.78e+01 1dbhA 354 -26.62 -3.47 2.87e+01 1fftC 204 -28.35 -3.46 2.89e+01 1fps 348 -28.68 -3.42 3.02e+01 1ai7A 209 -23.66 -3.42 3.03e+01 1aijL 281 -30.89 -3.41 3.05e+01 1hy7A 173 -23.26 -3.37 3.19e+01 1l5zA 155 -22.89 -3.34 3.33e+01 1dl5A 317 -24.43 -3.33 3.36e+01 1aoiC 116 -24.12 -3.33 3.37e+01 1b71A 191 -24.07 -3.27 3.59e+01 1f45B 197 -27.81 -3.25 3.70e+01 1e9xA 455 -26.14 -3.24 3.72e+01 1a28A 256 -26.29 -3.23 3.76e+01 1gm7A 209 -23.49 -3.23 3.77e+01 1dbqA 289 -24.28 -3.20 3.89e+01 1j4nA 271 -30.53 -3.20 3.92e+01 1bhb 71 -24.90 -3.20 3.93e+01 1au1A 166 -25.41 -3.18 3.97e+01