% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 09/03/03_16:30:36 % (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.YGR038C-B.t2k-100-30-CB_burial_14_7 Host: cc55 Mon Nov 17 23:16:54 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR038C-B % --------------------------------------------------------------------- % 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 ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR038C-B.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR038C-B.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8940 sequences, 2116673 residues, 1756 nodes, 2109.94 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 (=8162) sequences: % N / (1 + exp(-(lambda(=1.8128) * Reverse)^tau(=0.7170))) % 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 1asu 162 -94.80 -67.38 1.98e-10 1vsd 152 -88.21 -61.89 1.26e-09 1cxqA 162 -84.60 -58.44 4.15e-09 2itg 163 -75.64 -45.85 3.81e-07 1b9dA 163 -62.74 -36.00 1.68e-05 1exqA 154 -64.17 -36.00 1.68e-05 1hyvA 166 -61.75 -34.01 3.74e-05 1bl3A 160 -59.15 -32.90 5.87e-05 1itg 166 -56.17 -29.82 2.11e-04 1a1tA 55 -52.75 -22.19 5.91e-03 1f6uA 55 -54.63 -21.39 8.53e-03 1mfs 55 -55.04 -21.10 9.75e-03 1aaf 55 -53.90 -19.45 2.11e-02 1nc8 29 -40.73 -16.41 9.25e-02 1a6bB 40 -49.65 -15.45 1.50e-01 1dsqA 21 -34.64 -15.42 1.52e-01 1hvc 203 -41.46 -15.23 1.68e-01 1ffkZ 92 -48.11 -10.49 2.11e+00 1jj22 92 -48.85 -10.29 2.36e+00 1mml 265 -45.53 -9.86 3.02e+00 1cf9A 753 -63.77 -8.96 5.10e+00 1p80A 753 -63.58 -8.81 5.58e+00 1nf2A 268 -33.42 -8.12 8.41e+00 1qkkA 155 -34.58 -8.12 8.41e+00 1cl4A 60 -37.75 -7.80 1.02e+01 1ofuX 119 -31.07 -7.77 1.04e+01 1gseA 221 -39.25 -7.70 1.09e+01 1dsvA 31 -34.18 -7.62 1.14e+01 1ln1A 214 -38.01 -7.24 1.45e+01 1eduA 149 -32.93 -7.19 1.49e+01 1eyhA 144 -32.44 -7.09 1.59e+01 1gulA 222 -34.80 -6.99 1.69e+01 1f8vA 355 -41.71 -6.99 1.69e+01 1gm5A 780 -59.11 -6.99 1.70e+01 1dat 174 -33.19 -6.93 1.75e+01 1igtB 444 -52.99 -6.78 1.93e+01 1igtD 444 -53.09 -6.70 2.03e+01 1f2eA 201 -31.80 -6.63 2.13e+01 1gumA 222 -34.28 -6.52 2.28e+01 1exkA 79 -36.61 -6.44 2.41e+01 1jxcA 68 -32.89 -6.40 2.47e+01 1ltlA 279 -39.00 -6.28 2.67e+01 1mea 28 -28.33 -6.28 2.68e+01 1qs8A 329 -36.33 -6.24 2.75e+01 1h0aA 158 -32.32 -6.17 2.86e+01 2omf 340 -40.61 -6.13 2.94e+01 1k3yA 221 -36.37 -5.92 3.38e+01 1k3lA 221 -36.28 -5.91 3.40e+01 1b4pA 217 -38.73 -5.89 3.46e+01 1miqA 375 -39.97 -5.87 3.49e+01 1xjo 284 -31.04 -5.87 3.50e+01 1iz5A 249 -34.58 -5.85 3.53e+01 1aew 174 -33.37 -5.85 3.54e+01 1qvcA 145 -48.08 -5.78 3.72e+01 1bu5A 147 -28.41 -5.73 3.83e+01 1lvk 762 -54.24 -5.73 3.83e+01 1g5gB 481 -47.25 -5.72 3.86e+01 2asi 360 -37.23 -5.72 3.87e+01