% 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. % --------------------------------------------------------------------- % alphafoo.1.YGR235C.t2k-100-30-alpha Host: cc86 Tue Nov 12 19:01:39 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR235C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.alphas % % 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 YGR235C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR235C.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 234 nodes, 155.98 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(=2.5910) * Reverse)^tau(=0.7219))) % 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 1iq0A 592 -33.13 -11.08 9.17e-02 1sig 339 -32.55 -10.56 1.35e-01 1iwhB 146 -29.86 -10.23 1.73e-01 1jetA 517 -30.84 -8.31 7.64e-01 2olbA 517 -30.80 -8.23 8.09e-01 1jevA 517 -30.74 -8.19 8.36e-01 1asx 159 -28.27 -7.71 1.23e+00 1ass 159 -28.20 -7.52 1.44e+00 1fliA 98 -25.75 -7.38 1.61e+00 1hcnA 92 -25.11 -7.14 1.97e+00 1yme 309 -28.03 -6.85 2.52e+00 1g0u1 266 -27.37 -6.71 2.82e+00 1kl7A 514 -29.37 -6.56 3.22e+00 1wdb 104 -24.59 -6.48 3.44e+00 2ctc 307 -27.90 -6.44 3.56e+00 1ryp2 233 -26.70 -6.42 3.63e+00 2ctb 307 -27.63 -6.28 4.06e+00 1dz7A 92 -24.16 -6.23 4.27e+00 1necA 216 -27.36 -6.08 4.83e+00 6cpa 307 -27.11 -5.86 5.86e+00 1sur 215 -26.49 -5.81 6.11e+00 1fhjB 146 -26.33 -5.74 6.51e+00 1irdB 146 -25.59 -5.59 7.48e+00 1dxtB 147 -25.63 -5.54 7.76e+00 1babB 146 -25.68 -5.54 7.78e+00 2spcA 107 -25.24 -5.51 8.04e+00 1e69B 322 -27.95 -5.43 8.60e+00 1chuA 540 -28.24 -5.41 8.75e+00 1mgtA 174 -25.42 -5.39 8.90e+00 1fjgR 88 -23.46 -5.38 8.99e+00 1a6dA 545 -30.56 -5.38 9.01e+00 1blu 82 -22.66 -5.34 9.33e+00 1im4A 221 -25.37 -5.31 9.60e+00 1icrA 217 -25.83 -5.21 1.05e+01 1dmtA 696 -29.43 -5.20 1.06e+01 1c3wA 222 -25.44 -5.18 1.08e+01 1aep 161 -25.53 -5.16 1.09e+01 1spgB 147 -25.53 -5.12 1.14e+01 1smd 496 -26.92 -5.03 1.23e+01 1in6A 334 -26.58 -5.03 1.24e+01 1bob 320 -26.38 -4.89 1.40e+01 1l7vA 326 -29.48 -4.88 1.41e+01 1fjgC 239 -25.07 -4.84 1.47e+01 1j54A 186 -24.54 -4.83 1.48e+01 1b3qA 379 -26.49 -4.76 1.59e+01 1jenA 267 -26.03 -4.73 1.63e+01 1m0kA 262 -25.58 -4.72 1.64e+01 1kxlA 199 -24.99 -4.72 1.64e+01 1jfkA 134 -25.17 -4.65 1.75e+01 1i4jA 110 -22.75 -4.62 1.80e+01 1k2yX 463 -27.02 -4.58 1.87e+01 1cby 259 -25.64 -4.57 1.88e+01 1amuA 563 -27.09 -4.54 1.95e+01 1cyo 93 -22.23 -4.51 2.00e+01 1pszA 303 -25.85 -4.50 2.02e+01 2bds 43 -20.38 -4.47 2.08e+01 1hx0A 496 -26.46 -4.41 2.20e+01 1e5eA 404 -26.10 -4.39 2.24e+01 1ib8A 164 -23.34 -4.36 2.31e+01 1h2aL 567 -27.50 -4.34 2.35e+01 1i3dA 146 -25.14 -4.31 2.42e+01 1udg 244 -25.13 -4.31 2.43e+01 1seiA 130 -22.78 -4.28 2.48e+01 1jfuA 186 -23.30 -4.28 2.48e+01 1aqzB 149 -22.81 -4.27 2.51e+01 1jx4A 352 -27.30 -4.25 2.55e+01 1csn 298 -26.25 -4.22 2.63e+01 1bds 43 -20.16 -4.22 2.64e+01 1aqzA 149 -22.71 -4.21 2.65e+01 1amk 251 -25.17 -4.18 2.74e+01 1udh 244 -25.05 -4.18 2.75e+01 1lfpA 249 -24.88 -4.16 2.79e+01 1cot 129 -22.66 -4.16 2.79e+01 12asA 330 -25.25 -4.16 2.80e+01 1lq7A 67 -22.95 -4.13 2.88e+01 1kgbA 231 -24.57 -4.06 3.08e+01 1qhkA 47 -21.19 -4.05 3.10e+01 1qvaA 223 -24.02 -4.02 3.21e+01 1kmdA 117 -23.12 -4.00 3.26e+01 1zid 268 -24.85 -3.99 3.28e+01 1bxeA 113 -22.49 -3.96 3.38e+01 1j5eC 239 -24.28 -3.95 3.41e+01 2at9 247 -24.73 -3.94 3.47e+01 1dnlA 199 -23.17 -3.93 3.48e+01 1ajsA 412 -25.92 -3.93 3.48e+01 1aj0 282 -25.38 -3.92 3.52e+01 1ci8A 392 -25.42 -3.91 3.55e+01 1i0hA 205 -25.68 -3.89 3.62e+01 1a99A 344 -25.15 -3.89 3.63e+01 1jsdB 176 -23.76 -3.88 3.67e+01 1g4mA 393 -24.84 -3.88 3.67e+01 1jl0A 334 -25.76 -3.87 3.68e+01 1qgwC 177 -23.83 -3.86 3.73e+01 1cec 343 -25.16 -3.84 3.81e+01 1g99A 408 -25.44 -3.83 3.85e+01 1lay 256 -24.56 -3.81 3.94e+01 1spgA 144 -23.44 -3.80 3.97e+01