% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 07/18/05_14:54:13 % (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.YGR236C.t2k-100-30-CB_burial_14_7 Host: farm16.cse.ucsc.edu Fri Mar 3 09:07:18 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR236C % --------------------------------------------------------------------- % 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 YGR236C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR236C.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14381 sequences, 3373755 residues, 96 nodes, 159.57 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(=1.7270) * Reverse)^tau(=0.8163))) % 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 1urqA 63 -27.17 -10.97 1.77e-01 1rutX 188 -19.49 -9.31 7.09e-01 1enk 138 -19.33 -8.86 1.04e+00 1enj 138 -19.28 -8.83 1.06e+00 1eni 138 -19.34 -8.80 1.09e+00 1mroC 247 -21.00 -8.59 1.31e+00 1hbnC 248 -20.77 -8.54 1.37e+00 2end 138 -19.03 -8.53 1.38e+00 1vasA 137 -18.82 -8.40 1.54e+00 1vqsA 116 -19.78 -8.40 1.54e+00 1zsxA 347 -15.50 -6.95 5.48e+00 1uelB 48 -21.13 -6.91 5.68e+00 1yaxA 153 -18.05 -6.87 5.88e+00 1j9jA 247 -18.80 -6.81 6.23e+00 1pm6A 72 -22.18 -6.73 6.65e+00 1j9lA 247 -18.49 -6.66 7.12e+00 2a6qA 86 -22.37 -6.59 7.58e+00 1exbA 332 -14.83 -6.57 7.74e+00 1nfiA 301 -19.55 -6.56 7.77e+00 1ytfD 121 -21.62 -6.55 7.84e+00 1nvpD 108 -20.80 -6.55 7.84e+00 2cqeA 98 -20.43 -6.47 8.41e+00 1vk9A 151 -16.77 -6.32 9.69e+00 1nfiC 301 -19.57 -6.30 9.85e+00 1qrqA 325 -14.76 -6.25 1.03e+01 1nh2D 121 -21.10 -6.18 1.09e+01 1p9cA 45 -20.73 -6.17 1.11e+01 1e0fI 57 -17.51 -6.17 1.11e+01 2c3vA 102 -16.02 -6.15 1.13e+01 1gd8A 118 -16.07 -6.08 1.20e+01 1yx4A 132 -25.13 -6.02 1.28e+01 1nvpB 57 -19.99 -6.00 1.30e+01 1ifa 158 -16.34 -5.99 1.31e+01 2hfh 109 -17.88 -5.97 1.33e+01 1t7pA 698 -17.39 -5.94 1.36e+01 1rylA 167 -15.65 -5.85 1.48e+01 2d00A 109 -20.28 -5.70 1.70e+01 1ash 150 -16.02 -5.64 1.81e+01 2a23A 82 -15.84 -5.62 1.84e+01 1or7A 194 -18.84 -5.57 1.92e+01 2a4hA 126 -17.78 -5.57 1.93e+01 1g8eA 116 -20.11 -5.55 1.97e+01 1yfbA 59 -20.52 -5.43 2.20e+01 1a97A 148 -15.11 -5.33 2.40e+01 1s4bP 674 -14.54 -5.27 2.54e+01 2lhb 149 -14.83 -5.26 2.58e+01 1v5mA 136 -14.58 -5.14 2.87e+01 1z0rA 53 -19.10 -5.14 2.88e+01 1wu3I 161 -14.60 -5.13 2.92e+01 2aamA 309 -13.75 -5.13 2.92e+01 1im4A 221 -16.04 -5.12 2.92e+01 2cu6A 103 -14.74 -5.09 3.02e+01 1zvdA 380 -16.74 -5.01 3.26e+01 1yruB 74 -17.44 -4.98 3.35e+01 1x9mA 698 -17.56 -4.96 3.40e+01 1hcc 59 -16.23 -4.96 3.43e+01 2viuB 175 -21.62 -4.94 3.48e+01 3hmgB 175 -21.62 -4.94 3.49e+01 1dgrW 93 -21.63 -4.93 3.50e+01 1n13B 113 -15.21 -4.92 3.54e+01 2fe7A 166 -16.11 -4.92 3.55e+01 1hgeB 175 -21.62 -4.90 3.61e+01 1wspA 84 -15.28 -4.87 3.70e+01 1aoy 78 -16.95 -4.87 3.73e+01 1d3zA 76 -15.46 -4.86 3.75e+01 1lbvA 252 -13.07 -4.83 3.85e+01 1p9yA 121 -18.99 -4.83 3.87e+01 1f0mA 82 -14.88 -4.82 3.91e+01 2ax6A 256 -14.97 -4.79 4.00e+01