% SAM: /projects/compbio/bin/i686/hmmscore v3.3.2 (February, 2001) compiled 06/24/02_10:50:12 % (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-T99, 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, C. Barrett, R. Hughey, Hidden Markov models for detecting % remote protein homologies, Bioinformatics 14(10):846-856, 1998. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % dsspfoo.1.YGR022C.t2k-100-30-dssp-ebghstl Host: cc51 Fri Nov 8 17:19:41 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR022C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.dssps % % 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 YGR022C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR022C.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7310 sequences, 1706072 residues, 110 nodes, 73.67 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 (=7316) sequences: % N / (1 + exp(-(lambda(=2.4075) * Reverse)^tau(=0.7727))) % 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 1in6A 334 -30.08 -8.85 1.77e-01 1gpmA 525 -30.43 -8.50 2.46e-01 1in4A 334 -29.21 -7.98 4.00e-01 1l0wA 580 -28.79 -7.00 1.03e+00 1c7nA 399 -26.51 -5.78 3.48e+00 1pot 325 -26.57 -5.70 3.77e+00 1fts 295 -26.49 -5.64 4.01e+00 1faaA 124 -23.28 -5.60 4.20e+00 1gzgA 337 -26.82 -5.60 4.21e+00 1cnzA 363 -27.26 -5.49 4.72e+00 1b4kA 337 -26.49 -5.48 4.74e+00 1ykfA 352 -26.47 -5.23 6.12e+00 1iq4A 179 -25.06 -5.15 6.71e+00 1mpgA 282 -25.09 -5.14 6.77e+00 1d0yA 761 -27.44 -4.89 8.85e+00 1c0pA 363 -25.78 -4.85 9.15e+00 1evsA 187 -24.66 -4.79 9.79e+00 1lvk 762 -27.39 -4.69 1.09e+01 1itm 130 -22.69 -4.68 1.10e+01 1bbn 133 -22.65 -4.65 1.13e+01 1grj 158 -25.62 -4.61 1.19e+01 1rcb 129 -22.62 -4.60 1.20e+01 1jygA 69 -21.93 -4.52 1.31e+01 2int 129 -22.51 -4.47 1.37e+01 1hziA 129 -22.58 -4.44 1.42e+01 1h4wA 224 -23.42 -4.40 1.49e+01 1qe3A 489 -25.34 -4.35 1.57e+01 1mnd 762 -26.93 -4.34 1.59e+01 1d3bB 91 -20.94 -4.34 1.59e+01 1cm7A 363 -26.59 -4.32 1.63e+01 1kk1A 410 -25.13 -4.31 1.64e+01 1vom 762 -26.69 -4.26 1.74e+01 1jykA 254 -24.21 -4.24 1.78e+01 1nddA 76 -21.01 -4.16 1.94e+01 1ggwA 140 -23.37 -4.11 2.06e+01 1a6q 382 -25.13 -4.05 2.18e+01 1itf 165 -23.34 -4.04 2.20e+01 2sniI 83 -21.02 -4.04 2.21e+01 1bt0A 76 -20.86 -4.03 2.23e+01 1nddD 76 -20.88 -4.02 2.25e+01 1ayfB 105 -21.56 -4.01 2.28e+01 1qs2A 401 -24.46 -3.98 2.37e+01 2olbA 517 -24.91 -3.95 2.44e+01 1jevA 517 -24.85 -3.89 2.60e+01 1ayfA 105 -21.39 -3.86 2.71e+01 1ii5A 233 -23.08 -3.85 2.72e+01 2lfb 100 -21.19 -3.85 2.73e+01 1iiwA 232 -22.98 -3.83 2.81e+01 1b3tA 147 -21.94 -3.81 2.87e+01 1kevA 351 -25.98 -3.80 2.90e+01 1jndA 420 -25.15 -3.79 2.92e+01 1e8cA 498 -25.53 -3.76 3.00e+01 1pfo 500 -24.69 -3.75 3.04e+01 1jetA 517 -24.66 -3.71 3.20e+01 1lw6I 64 -20.41 -3.71 3.21e+01 1pedA 351 -25.85 -3.67 3.34e+01 1hznA 31 -17.79 -3.67 3.36e+01 1k3zD 282 -23.72 -3.62 3.52e+01 2cmkA 227 -23.37 -3.61 3.55e+01 1eqfA 280 -24.23 -3.58 3.69e+01 1bea 127 -21.36 -3.57 3.72e+01 1bwsA 321 -24.25 -3.55 3.84e+01 1go4E 100 -21.26 -3.54 3.89e+01