% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 06/01/06_09:03:53 % (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.YGR017W.t2k-100-30-CB_burial_14_7 Host: farm03-10.kilokluster.ucsc.edu Fri Oct 6 04:58:48 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR017W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/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 YGR017W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR017W.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 15583 sequences, 3659059 residues, 298 nodes, 461.92 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(=1.4211) * Reverse)^tau(=0.8142))) % 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 2i51A 195 -230.30 -214.27 2.21e-42 1t9mA 214 -68.88 -53.20 2.20e-11 1ty9A 222 -60.27 -44.95 1.69e-09 1nrgA 261 -58.58 -42.69 5.68e-09 1dnlA 199 -50.39 -35.21 3.46e-07 1g79A 218 -48.99 -34.06 6.58e-07 1ci0A 228 -42.51 -23.66 2.78e-04 2a2jA 246 -40.98 -23.39 3.25e-04 1rfeA 162 -25.19 -13.05 2.29e-01 1egxA 115 -22.61 -12.24 3.96e-01 2i02A 148 -25.46 -12.07 4.44e-01 1i6pA 220 -23.52 -10.41 1.40e+00 2av1A 275 -22.09 -9.78 2.19e+00 2av7A 275 -21.90 -9.71 2.29e+00 1hsbA 270 -22.60 -9.57 2.54e+00 1duzA 275 -21.84 -9.30 3.09e+00 1xccA 220 -22.25 -9.14 3.44e+00 1k5nA 276 -21.67 -9.01 3.80e+00 1i4fA 275 -20.94 -8.85 4.25e+00 1agdA 276 -21.02 -8.44 5.73e+00 1hocA 272 -21.87 -8.37 6.05e+00 2bvpA 276 -19.92 -8.11 7.32e+00 2aq6A 147 -19.53 -8.05 7.60e+00 1m7sA 484 -22.83 -7.92 8.37e+00 1sesA 421 -21.46 -7.54 1.11e+01 1h4aX 173 -17.98 -7.42 1.21e+01 1pjqA 457 -21.70 -7.41 1.23e+01 1uv7A 110 -22.17 -7.26 1.37e+01 1aa0 113 -30.67 -7.25 1.38e+01 1u5tC 202 -22.46 -7.22 1.41e+01 1xxoA 147 -19.27 -7.21 1.42e+01 1w2wB 191 -23.45 -7.16 1.48e+01 1l8qA 324 -18.53 -7.07 1.58e+01 1jzuA 157 -20.28 -7.05 1.61e+01 1gvnA 90 -19.05 -7.02 1.65e+01 1knzA 164 -29.97 -6.97 1.70e+01 1qbhA 101 -22.32 -6.86 1.84e+01 2asfA 137 -17.17 -6.83 1.89e+01 1w9aA 147 -19.24 -6.77 1.99e+01 1avyA 74 -27.14 -6.76 1.99e+01 1a9eA 277 -19.11 -6.66 2.16e+01 1a1oA 276 -19.01 -6.50 2.43e+01 1bcsB 160 -24.14 -6.44 2.54e+01 2bnxA 386 -28.08 -6.43 2.58e+01 1evhA 112 -17.51 -6.41 2.61e+01 1whsA 255 -18.87 -6.38 2.67e+01 1avyC 74 -27.05 -6.37 2.70e+01 2f66C 82 -24.66 -6.35 2.73e+01 1opaA 135 -19.60 -6.30 2.84e+01 1whtB 153 -23.93 -6.29 2.87e+01 1nkiA 135 -19.50 -6.26 2.93e+01 1hjbA 87 -26.59 -6.25 2.95e+01 1bcsA 263 -18.91 -6.24 2.97e+01 1j1jA 240 -20.18 -6.19 3.09e+01 1avyB 74 -25.13 -6.14 3.20e+01 1xb4A 202 -19.83 -6.14 3.21e+01 1whsB 153 -23.69 -6.13 3.25e+01 1a17 166 -22.26 -6.11 3.27e+01 1a1mA 278 -18.91 -6.11 3.27e+01 1whtA 256 -18.38 -6.10 3.31e+01 1lqpA 135 -19.46 -6.08 3.35e+01 2dafA 118 -19.54 -6.03 3.48e+01 1v54F 98 -23.24 -6.02 3.52e+01 1emwA 88 -18.45 -6.02 3.53e+01 1oxa 403 -16.35 -5.97 3.65e+01 1gu4A 78 -25.60 -5.94 3.75e+01 1kjvA 284 -18.53 -5.94 3.76e+01 1j8uA 325 -16.47 -5.92 3.81e+01 1fioA 196 -18.38 -5.89 3.91e+01 1af3 196 -18.33 -5.88 3.92e+01