% 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.YGR016W.t2k-100-30-alpha Host: cc41 Fri Nov 8 17:10:40 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR016W % --------------------------------------------------------------------- % 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 YGR016W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR016W.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7310 sequences, 1706072 residues, 191 nodes, 127.69 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(=2.5371) * Reverse)^tau(=0.7409))) % 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 1g5hA 454 -32.16 -9.70 1.59e-01 1g99A 408 -29.12 -7.88 7.40e-01 1qj4A 257 -28.25 -7.83 7.75e-01 1yasA 257 -28.31 -7.82 7.80e-01 1kr4A 125 -24.56 -6.51 2.48e+00 1knqA 175 -26.71 -6.34 2.91e+00 1b43A 340 -27.36 -6.15 3.45e+00 1h8eA 510 -28.60 -6.10 3.60e+00 1e79A 510 -28.46 -6.00 3.99e+00 1bmfA 510 -28.81 -5.99 4.02e+00 1qklA 127 -24.32 -5.86 4.52e+00 1howA 373 -27.19 -5.80 4.78e+00 1hv2A 99 -24.79 -5.74 5.07e+00 1hzpA 335 -26.06 -5.72 5.13e+00 1yprA 125 -24.63 -5.68 5.36e+00 1i6uA 130 -23.99 -5.68 5.37e+00 1hnoA 280 -27.12 -5.67 5.42e+00 1fliA 98 -23.98 -5.61 5.72e+00 1hnuA 280 -27.01 -5.57 5.93e+00 1lmb3 92 -23.27 -5.45 6.65e+00 1lliA 92 -23.04 -5.25 8.05e+00 1ukz 203 -25.44 -4.92 1.11e+01 1go5A 69 -22.03 -4.79 1.25e+01 1dfaA 454 -26.42 -4.72 1.35e+01 1jflA 228 -24.92 -4.56 1.58e+01 1spgA 144 -25.42 -4.55 1.60e+01 1awcA 110 -22.81 -4.54 1.61e+01 1i7dA 659 -27.33 -4.53 1.63e+01 4sgbI 51 -20.08 -4.51 1.66e+01 1gwcA 230 -26.10 -4.50 1.68e+01 1pbwA 216 -24.92 -4.49 1.70e+01 1aw5 326 -25.63 -4.47 1.73e+01 1ezvE 185 -23.96 -4.43 1.81e+01 1ap6A 198 -24.22 -4.36 1.94e+01 1dofA 403 -26.32 -4.28 2.09e+01 1gv3A 248 -24.95 -4.27 2.11e+01 1abmA 198 -24.20 -4.25 2.15e+01 1fpqA 372 -26.30 -4.25 2.17e+01 1fp1D 372 -26.11 -4.24 2.18e+01 1gg3A 279 -24.56 -4.22 2.21e+01 1d2zB 153 -23.97 -4.18 2.31e+01 1c8bA 371 -25.31 -4.18 2.31e+01 1ffkC 246 -24.38 -4.16 2.37e+01 1qsdA 106 -23.56 -4.14 2.41e+01 1f44A 324 -24.84 -4.08 2.56e+01 3nul 130 -22.90 -4.08 2.58e+01 1kwsA 261 -23.49 -3.99 2.82e+01 1k3zD 282 -24.53 -3.97 2.88e+01 1hyhA 309 -25.02 -3.97 2.88e+01 1lldA 319 -25.18 -3.91 3.05e+01 1et0A 269 -25.58 -3.90 3.08e+01 1a0k 131 -22.75 -3.86 3.21e+01 1rie 129 -22.72 -3.86 3.23e+01 1mof 55 -20.72 -3.84 3.29e+01 2rspB 124 -23.35 -3.84 3.29e+01 1preA 470 -25.07 -3.82 3.36e+01 1lqvA 193 -23.85 -3.82 3.37e+01 1fybA 111 -21.34 -3.81 3.37e+01 1b6g 310 -25.42 -3.81 3.39e+01 1fu9A 36 -19.41 -3.81 3.40e+01 1ek8A 185 -23.22 -3.77 3.52e+01 1ede 310 -25.40 -3.76 3.56e+01 1j5yA 187 -23.36 -3.76 3.57e+01 1fggA 261 -23.28 -3.76 3.57e+01 1jj2C 246 -24.09 -3.72 3.72e+01 2pcfB 250 -23.51 -3.70 3.80e+01 1gj7B 253 -23.41 -3.70 3.81e+01 1j8eA 44 -19.48 -3.70 3.82e+01