% 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. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YGR024C.t2k-100-30-dssp-ehl2 Host: cc69 Fri Nov 8 18:06:30 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR024C % --------------------------------------------------------------------- % 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 YGR024C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR024C.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7310 sequences, 1706072 residues, 238 nodes, 161.27 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(=1.3322) * Reverse)^tau(=0.8406))) % 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 1qgwC 177 -31.79 -11.28 4.25e-01 1ezm 301 -34.10 -10.51 7.46e-01 1k2yX 463 -33.92 -10.45 7.79e-01 1hbq 183 -30.14 -9.09 2.15e+00 1hbp 183 -30.18 -8.97 2.34e+00 1aqb 183 -29.97 -8.84 2.58e+00 1qkmA 255 -31.03 -8.13 4.44e+00 1jp3A 253 -30.56 -8.02 4.81e+00 1hv8A 367 -32.20 -7.92 5.19e+00 1eu8A 409 -31.02 -7.88 5.35e+00 1cuk 203 -29.87 -7.77 5.85e+00 1k3eA 156 -29.48 -7.75 5.95e+00 1exnA 290 -30.61 -7.54 6.97e+00 1exnB 290 -30.64 -7.52 7.08e+00 1lox 662 -31.77 -7.51 7.13e+00 1g24A 211 -28.14 -7.50 7.18e+00 3cla 213 -28.16 -7.38 7.91e+00 1pyaB 228 -28.50 -7.32 8.29e+00 1cnt2 187 -29.83 -7.27 8.58e+00 1ekeA 230 -29.48 -7.26 8.67e+00 1bed 181 -28.96 -7.15 9.46e+00 1io2A 213 -28.94 -7.12 9.71e+00 1hjp 203 -29.93 -7.11 9.71e+00 1hm6A 346 -29.78 -7.02 1.04e+01 1yuiA 54 -23.30 -6.97 1.09e+01 1efnB 152 -26.28 -6.83 1.21e+01 1cb6A 691 -30.77 -6.76 1.28e+01 1aokB 122 -25.92 -6.71 1.33e+01 1c1dA 355 -28.69 -6.69 1.36e+01 1cc1L 498 -29.91 -6.66 1.38e+01 1a0p 290 -29.48 -6.62 1.44e+01 1fntc 245 -28.66 -6.61 1.45e+01 1rbp 182 -27.52 -6.59 1.47e+01 1lx7A 253 -27.73 -6.58 1.48e+01 1brlB 324 -29.36 -6.57 1.49e+01 1jyoA 130 -26.63 -6.56 1.51e+01 1qlpA 394 -28.65 -6.52 1.55e+01 1atzB 189 -26.95 -6.50 1.58e+01 1jeyA 609 -30.39 -6.46 1.62e+01 1fe8A 196 -26.92 -6.46 1.63e+01 1crxA 322 -30.11 -6.44 1.66e+01 1khvA 516 -32.35 -6.43 1.66e+01 1ig0A 319 -28.52 -6.37 1.75e+01 1bw9A 356 -29.08 -6.37 1.75e+01 1pfkA 320 -29.06 -6.37 1.75e+01 1pvdA 537 -30.19 -6.36 1.76e+01 1pydA 556 -30.20 -6.31 1.84e+01 1ryt 190 -29.14 -6.26 1.91e+01 1a8y 367 -29.60 -6.25 1.91e+01 1f44A 324 -30.02 -6.25 1.92e+01 1dvbA 191 -29.14 -6.25 1.92e+01 1atzA 189 -26.68 -6.23 1.95e+01 1kbuA 349 -30.54 -6.17 2.05e+01 1cxqA 162 -26.86 -6.14 2.11e+01 3crxA 343 -30.50 -6.11 2.16e+01 9apiA 347 -28.23 -6.05 2.25e+01 1qpbA 563 -29.77 -6.04 2.27e+01 1go4A 205 -31.47 -6.04 2.28e+01 1k8kA 418 -28.96 -6.04 2.28e+01 1kq4A 232 -28.92 -5.99 2.37e+01 2pfkA 320 -28.70 -5.96 2.42e+01 2hmiA 558 -31.07 -5.95 2.44e+01 1fwyA 331 -28.34 -5.95 2.45e+01 1rpl 251 -27.58 -5.93 2.47e+01 1f2tB 148 -29.36 -5.93 2.48e+01 1lucB 324 -28.83 -5.91 2.52e+01 1hv9A 456 -28.74 -5.86 2.62e+01 4crxA 322 -29.84 -5.85 2.64e+01 1dkgD 383 -28.59 -5.82 2.72e+01 1b71A 191 -28.68 -5.72 2.93e+01 1rypF 233 -27.86 -5.71 2.96e+01 1gaxA 862 -31.05 -5.70 2.98e+01 1i3dA 146 -26.47 -5.70 3.00e+01 1aba 87 -23.84 -5.69 3.00e+01 1eq2A 310 -28.03 -5.69 3.00e+01 1vsd 152 -26.03 -5.68 3.04e+01 1ihfA 99 -24.55 -5.66 3.09e+01 1fjgI 128 -25.29 -5.64 3.15e+01 1dgqA 188 -28.92 -5.63 3.16e+01 1asu 162 -26.17 -5.62 3.18e+01 1jltB 122 -25.09 -5.55 3.36e+01 1k8eA 345 -27.13 -5.54 3.41e+01 1dt6A 473 -30.58 -5.52 3.46e+01 1l2iA 261 -28.22 -5.47 3.61e+01 1d8dA 377 -28.22 -5.45 3.66e+01 1p35A 299 -28.02 -5.45 3.67e+01 1ip9A 85 -24.24 -5.43 3.72e+01 1jcrA 377 -28.17 -5.42 3.76e+01 3bifA 468 -29.02 -5.36 3.93e+01 1hqkA 154 -27.23 -5.36 3.94e+01 1bif 469 -28.97 -5.35 3.98e+01