% 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.YGR035W-A.t2k-100-30-CB_burial_14_7 Host: farm09.cse.ucsc.edu Sun Feb 12 22:13:25 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR035W-A % --------------------------------------------------------------------- % 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 YGR035W-A.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR035W-A.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13614 sequences, 3208521 residues, 74 nodes, 116.85 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(=2.6004) * Reverse)^tau(=0.7649))) % 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 1aayA 90 -17.45 -9.16 1.36e-01 1zaaC 87 -17.33 -9.06 1.48e-01 1a1iA 90 -17.48 -9.01 1.57e-01 1jnrB 150 -18.29 -8.13 3.64e-01 1a0hA 159 -17.65 -7.73 5.35e-01 1g2fC 90 -15.28 -6.90 1.23e+00 2a4hA 126 -15.24 -6.62 1.63e+00 1llmC 88 -14.92 -6.41 2.02e+00 1g8oA 310 -13.44 -5.98 3.13e+00 1vr7A 142 -13.61 -5.89 3.45e+00 1xxsA 122 -14.85 -5.38 5.91e+00 1gx4A 289 -12.71 -5.22 7.03e+00 1iqyA 638 -13.76 -5.02 8.71e+00 1ui7A 638 -13.70 -5.01 8.89e+00 1ivwA 638 -13.72 -5.00 8.95e+00 1w6gA 646 -13.71 -4.97 9.26e+00 1rjoA 646 -13.71 -4.96 9.38e+00 1ui8A 638 -13.72 -4.95 9.46e+00 1avk 638 -13.71 -4.93 9.66e+00 1o7qA 289 -12.23 -4.82 1.08e+01 1tzpA 255 -12.86 -4.80 1.12e+01 1eeqA 114 -12.92 -4.77 1.16e+01 1wthD 391 -12.96 -4.76 1.16e+01 1eeuA 114 -12.91 -4.76 1.17e+01 1siiA 646 -13.45 -4.72 1.21e+01 1k4vA 289 -12.06 -4.72 1.22e+01 2aw4R 103 -12.86 -4.72 1.22e+01 1tluA 130 -12.43 -4.70 1.24e+01 1qbhA 101 -13.58 -4.67 1.28e+01 2cszA 76 -16.04 -4.57 1.43e+01 1jfuA 186 -11.77 -4.54 1.48e+01 2aw4Z 70 -14.22 -4.54 1.48e+01 1b6rA 355 -13.07 -4.50 1.55e+01 1plfA 72 -12.42 -4.50 1.56e+01 1tfi 50 -13.03 -4.47 1.60e+01 1k28D 391 -13.21 -4.43 1.67e+01 1rlyA 60 -14.78 -4.43 1.68e+01 1taq 832 -12.88 -4.42 1.70e+01 1yk3A 210 -12.19 -4.37 1.78e+01 2bl5A 140 -12.88 -4.37 1.80e+01 1meyC 87 -13.25 -4.29 1.97e+01 4rxn 54 -13.36 -4.20 2.17e+01 1nciA 110 -12.27 -4.18 2.22e+01 1y4hA 188 -12.52 -4.15 2.29e+01 1rhoC 145 -12.26 -4.07 2.51e+01 1zfuA 40 -13.25 -4.06 2.54e+01 1pxvA 183 -12.32 -4.06 2.55e+01 1y4lA 121 -13.39 -4.00 2.73e+01 1ois 223 -13.60 -3.99 2.77e+01 1ncg 110 -12.13 -3.96 2.85e+01 1wf9A 107 -12.25 -3.93 2.94e+01 1n0wB 35 -13.39 -3.93 2.96e+01 1xaoA 121 -12.92 -3.90 3.05e+01 1pv9A 348 -12.38 -3.89 3.11e+01 1tc5A 194 -13.43 -3.89 3.11e+01 1fb6A 105 -12.42 -3.87 3.17e+01 1nozA 388 -11.82 -3.86 3.20e+01 1b6sA 355 -12.19 -3.84 3.27e+01 1yc61 154 -11.96 -3.83 3.32e+01 1jmxG 79 -13.62 -3.82 3.35e+01 1tw6A 133 -12.79 -3.82 3.35e+01 1k1gA 131 -12.96 -3.79 3.47e+01 1hzdA 272 -12.41 -3.79 3.48e+01 1gd8A 118 -11.73 -3.78 3.52e+01 1dl6A 58 -14.73 -3.77 3.57e+01 1yr0A 175 -11.40 -3.73 3.72e+01 1lldA 319 -11.53 -3.69 3.88e+01 1udg 244 -11.85 -3.67 3.99e+01