% 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.YGR016W.t2k-100-30-dssp-ebghstl Host: cc41 Fri Nov 8 17:02:01 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.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 YGR016W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR016W.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7310 sequences, 1706072 residues, 191 nodes, 128.23 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(=1.7420) * Reverse)^tau(=0.7910))) % 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 1g99A 408 -31.50 -8.93 1.14e+00 1lmb3 92 -27.26 -8.69 1.38e+00 1yasA 257 -29.68 -8.69 1.38e+00 1yprA 125 -28.27 -8.59 1.49e+00 1lliA 92 -26.89 -8.40 1.73e+00 1dofA 403 -31.55 -8.39 1.75e+00 1qj4A 257 -29.15 -8.24 1.96e+00 1g5hA 454 -31.27 -8.14 2.12e+00 1b43A 340 -30.05 -8.02 2.33e+00 1f00I 282 -27.63 -7.88 2.61e+00 1hzpA 335 -28.44 -7.77 2.84e+00 1ukz 203 -29.35 -7.70 3.02e+00 1go5A 69 -25.13 -7.05 5.07e+00 1knqA 175 -29.48 -6.92 5.66e+00 1eyeA 280 -28.11 -6.89 5.82e+00 1ap6A 198 -27.86 -6.79 6.27e+00 1howA 373 -28.95 -6.68 6.90e+00 1hv2A 99 -27.46 -6.66 7.00e+00 1bmfA 510 -29.82 -6.65 7.07e+00 1abmA 198 -27.97 -6.54 7.71e+00 1hnuA 280 -29.02 -6.52 7.87e+00 1hnoA 280 -28.72 -6.45 8.34e+00 1i7gA 287 -29.02 -6.33 9.24e+00 1jflA 228 -27.24 -6.30 9.44e+00 1a0k 131 -25.77 -6.04 1.18e+01 1awcA 110 -24.71 -5.93 1.29e+01 3nul 130 -25.61 -5.85 1.37e+01 1tahA 318 -28.78 -5.84 1.39e+01 1fp1D 372 -29.31 -5.76 1.48e+01 1gwcA 230 -28.91 -5.59 1.72e+01 2btfA 375 -27.27 -5.55 1.78e+01 1gg3A 279 -27.11 -5.53 1.81e+01 1poiA 317 -27.09 -5.43 1.96e+01 1h8eA 510 -29.14 -5.40 2.02e+01 1reqB 637 -28.50 -5.39 2.04e+01 1reqD 637 -28.47 -5.33 2.14e+01 1dgaA 375 -27.43 -5.33 2.15e+01 1e3jA 352 -28.21 -5.31 2.19e+01 1d4xA 375 -27.40 -5.28 2.24e+01 1qklA 127 -24.56 -5.21 2.38e+01 1e79A 510 -28.84 -5.20 2.40e+01 1pbwA 216 -26.66 -5.20 2.41e+01 1tahB 318 -28.00 -5.11 2.61e+01 1g19A 350 -26.85 -5.11 2.61e+01 1yagA 375 -27.34 -5.09 2.65e+01 1dcnD 436 -29.28 -5.08 2.67e+01 1eciA 37 -21.35 -5.07 2.68e+01 1fpqA 372 -28.96 -5.05 2.75e+01 1hskA 326 -26.83 -5.04 2.75e+01 1fggA 261 -24.71 -5.04 2.75e+01 1kwsA 261 -24.70 -5.02 2.81e+01 2pcfB 250 -25.19 -5.02 2.81e+01 1lldA 319 -27.62 -4.99 2.89e+01 1k8kA 418 -27.89 -4.96 2.96e+01 1f44A 324 -26.64 -4.94 3.02e+01 1cjaA 342 -27.96 -4.92 3.06e+01 1pyaB 228 -25.92 -4.91 3.10e+01 1gpuA 680 -29.19 -4.86 3.23e+01 1kafA 108 -23.48 -4.81 3.38e+01 1e5uI 187 -24.09 -4.80 3.41e+01 1mnmA 100 -24.41 -4.79 3.43e+01 3pflA 759 -29.17 -4.77 3.49e+01 1spgA 144 -27.10 -4.75 3.57e+01 1hcz 252 -25.19 -4.72 3.66e+01 1bh5A 183 -24.61 -4.71 3.69e+01 1fcdC 174 -24.07 -4.71 3.69e+01 1dcnA 424 -28.54 -4.67 3.83e+01 1qipA 183 -24.58 -4.67 3.84e+01 1cm5A 759 -29.11 -4.66 3.86e+01