% 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.YGR034W.t2k-100-30-CB_burial_14_7 Host: farm20 Wed Nov 17 18:58:59 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR034W % --------------------------------------------------------------------- % 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 YGR034W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR034W.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10772 sequences, 2550165 residues, 130 nodes, 140.05 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(=2.0157) * Reverse)^tau(=0.7317))) % 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 1s72T 120 -108.89 -93.19 1.01e-16 1jj2S 119 -108.34 -92.66 1.23e-16 1ffkQ 119 -105.99 -91.28 2.03e-16 1ri9A 102 -20.94 -8.75 3.05e+00 1hjdA 101 -18.54 -8.54 3.52e+00 1jj2X 240 -24.58 -8.35 3.99e+00 1s72Y 241 -24.25 -8.24 4.31e+00 1s72S 85 -17.37 -8.23 4.35e+00 1jj2R 84 -17.40 -8.06 4.89e+00 1uunA 184 -30.08 -8.06 4.91e+00 1ffkP 84 -16.76 -7.77 6.00e+00 1tjlA 151 -23.24 -7.75 6.06e+00 1irp 153 -17.35 -7.73 6.15e+00 1ffkV 143 -23.02 -7.41 7.74e+00 1ibyA 112 -18.63 -7.37 7.97e+00 1ibzA 112 -18.78 -7.21 8.91e+00 1g0sA 209 -24.45 -7.18 9.13e+00 2itg 163 -17.19 -7.16 9.26e+00 1g5rA 196 -15.77 -7.10 9.65e+00 2dynA 122 -17.13 -7.09 9.73e+00 1g19A 350 -18.46 -6.95 1.08e+01 1i3jA 116 -30.08 -6.78 1.22e+01 1b8zA 90 -23.68 -6.60 1.39e+01 1iraX 152 -16.02 -6.59 1.40e+01 1g5tA 196 -15.31 -6.48 1.52e+01 1bwzA 274 -14.61 -6.39 1.62e+01 1dynA 125 -15.78 -6.38 1.63e+01 1idiA 74 -17.57 -6.33 1.70e+01 1tfe 145 -18.04 -6.31 1.72e+01 1d7qA 143 -21.47 -6.16 1.93e+01 1e1oA 504 -17.61 -6.06 2.08e+01 1whsB 153 -26.04 -6.03 2.12e+01 1lnqA 336 -17.55 -6.01 2.15e+01 1whtB 153 -26.01 -6.00 2.17e+01 1k8kG 151 -18.76 -5.99 2.19e+01 1bcsB 160 -25.54 -5.97 2.23e+01 1ubeA 349 -17.91 -5.93 2.29e+01 2cuaA 135 -14.86 -5.93 2.30e+01 1ilr1 152 -15.13 -5.90 2.35e+01 2if1 126 -24.26 -5.82 2.50e+01 1ugpB 226 -25.21 -5.76 2.61e+01 1hl6A 165 -21.89 -5.75 2.63e+01 1fhuA 320 -13.51 -5.73 2.67e+01 1awo 62 -17.50 -5.70 2.73e+01 1t6aA 126 -26.46 -5.70 2.73e+01 1ov3A 138 -29.10 -5.68 2.78e+01 1ireB 228 -25.12 -5.68 2.78e+01 1dzfA 215 -15.43 -5.63 2.89e+01 1gqzA 274 -13.97 -5.61 2.93e+01 1b8aA 438 -14.44 -5.48 3.23e+01 1lylA 504 -17.40 -5.47 3.26e+01 1no1A 126 -17.48 -5.47 3.26e+01 2wrpR 107 -26.64 -5.43 3.35e+01 1bqv 110 -20.87 -5.43 3.36e+01 1a2xB 47 -22.06 -5.42 3.38e+01 1s72Q 96 -20.53 -5.41 3.43e+01 1qhxA 178 -13.97 -5.35 3.57e+01 1qqp3 220 -22.66 -5.34 3.60e+01 4rhv1 289 -24.43 -5.28 3.78e+01 1faaA 124 -14.82 -5.27 3.79e+01 1qexA 288 -21.32 -5.23 3.94e+01 1auiA 521 -20.08 -5.23 3.94e+01 1bbt3 220 -22.37 -5.22 3.94e+01