% 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. % --------------------------------------------------------------------- % strfoo.1.YEL010W.t2k-100-30-str Host: cc70 Mon Nov 11 06:24:33 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YEL0/YEL010W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.strs % % 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 YEL010W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YEL010W.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 117 nodes, 79.99 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(=1.4675) * Reverse)^tau(=0.8379))) % 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 1cviA 342 -35.33 -11.72 1.43e-01 2hpaA 342 -34.36 -11.08 2.35e-01 1fxoA 293 -31.41 -10.79 2.95e-01 1quqB 121 -30.38 -10.23 4.56e-01 1h5rA 293 -30.22 -9.59 7.64e-01 1g0rA 293 -28.99 -8.89 1.35e+00 1rpa 342 -32.10 -8.66 1.62e+00 1bet 107 -29.52 -8.24 2.29e+00 2pldA 105 -26.58 -8.03 2.70e+00 1ah6 220 -28.40 -7.42 4.48e+00 1bia 321 -29.09 -7.06 6.08e+00 1d2kA 392 -28.33 -6.85 7.27e+00 1gyxA 76 -24.06 -6.76 7.82e+00 1bib 321 -28.68 -6.75 7.90e+00 3vtk 343 -27.17 -6.73 8.05e+00 1bncB 449 -28.72 -6.69 8.30e+00 1dv1A 449 -28.75 -6.63 8.74e+00 1lbvA 252 -26.61 -6.33 1.13e+01 1hs6A 611 -34.23 -6.29 1.17e+01 1a8p 258 -26.24 -6.29 1.17e+01 1bcpF 99 -24.88 -6.14 1.33e+01 1prtF 98 -25.12 -6.08 1.40e+01 2pleA 105 -23.29 -6.06 1.42e+01 1rypJ 204 -28.73 -6.06 1.42e+01 1mmsA 140 -24.89 -6.05 1.43e+01 1g0uI 205 -28.69 -6.04 1.44e+01 1d0nA 729 -29.50 -5.99 1.52e+01 2rslA 140 -24.00 -5.92 1.61e+01 1k7wA 468 -27.93 -5.90 1.63e+01 1a6jA 163 -25.30 -5.89 1.65e+01 1rypH 205 -26.24 -5.84 1.73e+01 1uok 558 -28.00 -5.80 1.79e+01 1gdtA 183 -26.07 -5.72 1.91e+01 1hcl 298 -26.32 -5.70 1.94e+01 1dcnD 436 -27.72 -5.67 2.00e+01 1a6wL 109 -25.57 -5.66 2.01e+01 1e1xA 299 -26.19 -5.61 2.10e+01 1bolA 222 -27.45 -5.59 2.13e+01 1dkzA 219 -27.64 -5.55 2.21e+01 1auwA 468 -27.58 -5.53 2.25e+01 1vppV 102 -27.60 -5.53 2.26e+01 1f3yA 165 -24.37 -5.49 2.34e+01 1jvpP 298 -26.18 -5.42 2.47e+01 1bag 425 -26.21 -5.41 2.51e+01 1id0A 152 -24.79 -5.40 2.52e+01 1gnhA 206 -26.91 -5.34 2.66e+01 1a6uL 108 -25.07 -5.34 2.66e+01 1eg5A 384 -26.58 -5.29 2.77e+01 1gatA 60 -20.76 -5.28 2.79e+01 1wapA 75 -23.42 -5.27 2.82e+01 1i50B 1224 -33.52 -5.26 2.85e+01 1byqA 228 -26.06 -5.25 2.88e+01 1ig8A 486 -28.42 -5.25 2.89e+01 1bncA 449 -27.30 -5.24 2.90e+01 1ecxA 384 -26.69 -5.23 2.92e+01 1bftA 101 -23.09 -5.23 2.93e+01 1dkxA 219 -27.41 -5.23 2.94e+01 3lck 271 -26.03 -5.22 2.95e+01 3gatA 66 -20.89 -5.18 3.05e+01 2gatA 66 -20.80 -5.10 3.27e+01 1fj2A 232 -24.66 -5.10 3.29e+01 1h99A 224 -25.39 -5.09 3.32e+01 1yer 228 -26.21 -5.09 3.33e+01 1huxA 270 -25.74 -5.07 3.36e+01 1iqaA 160 -25.71 -5.00 3.60e+01 487dL 133 -23.25 -4.96 3.72e+01 1gzgA 337 -24.70 -4.95 3.76e+01 1h5qA 265 -24.95 -4.93 3.81e+01 1dqaA 467 -27.18 -4.91 3.90e+01 1svpA 161 -24.53 -4.88 3.98e+01