% 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.YGR030C.t2k-100-30-dssp-ehl2 Host: cc50 Fri Nov 8 18:45:57 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR030C % --------------------------------------------------------------------- % 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 YGR030C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR030C.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 159 nodes, 107.17 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(=1.6025) * Reverse)^tau(=0.7822))) % 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 1mldA 314 -33.79 -10.67 7.28e-01 1preB 470 -32.42 -9.60 1.51e+00 1preA 470 -31.39 -8.83 2.59e+00 1qfrA 89 -26.75 -7.97 4.79e+00 1mdl 359 -29.07 -7.57 6.36e+00 1jqeA 292 -32.21 -7.54 6.52e+00 1ptf 88 -26.21 -7.50 6.72e+00 2mnr 357 -28.94 -7.41 7.14e+00 1dkuA 317 -29.86 -7.11 8.93e+00 1cznA 169 -29.74 -6.93 1.02e+01 1ofv 169 -29.74 -6.93 1.02e+01 1a26 361 -28.12 -6.89 1.05e+01 1gk8A 475 -29.21 -6.81 1.12e+01 1dkrA 317 -29.82 -6.77 1.15e+01 1k7hA 476 -28.42 -6.75 1.16e+01 1efyA 350 -27.82 -6.73 1.19e+01 1ibsA 317 -29.72 -6.70 1.21e+01 1ig8A 486 -30.96 -6.50 1.41e+01 1gt7A 274 -27.38 -6.47 1.44e+01 1e4fT 419 -28.16 -6.37 1.55e+01 1bn7A 294 -27.37 -6.34 1.59e+01 1cqwA 295 -27.38 -6.33 1.59e+01 1bn6A 294 -27.51 -6.33 1.60e+01 1tubA 440 -29.14 -6.22 1.73e+01 1qguB 519 -29.33 -6.22 1.74e+01 1qh8B 519 -29.33 -6.21 1.75e+01 1kk1A 410 -28.35 -6.17 1.80e+01 8rucA 475 -28.48 -6.12 1.88e+01 1fkx 349 -29.14 -6.05 1.97e+01 1a4mA 349 -28.99 -5.99 2.08e+01 1f7cA 231 -25.76 -5.86 2.29e+01 1rcf 169 -29.49 -5.84 2.32e+01 1ihmA 530 -28.55 -5.74 2.50e+01 1nsf 273 -28.35 -5.67 2.65e+01 1qfoC 119 -24.09 -5.63 2.73e+01 1auz 116 -25.44 -5.60 2.80e+01 1jkmB 361 -27.81 -5.58 2.84e+01 1a7aA 432 -27.58 -5.58 2.85e+01 1caj 260 -27.05 -5.52 2.97e+01 1jffA 451 -29.38 -5.52 2.98e+01 1jkmA 358 -27.70 -5.51 2.99e+01 1bla 155 -24.66 -5.49 3.04e+01 1cjsA 219 -26.94 -5.47 3.09e+01 1hy3A 294 -26.00 -5.37 3.34e+01 2gar 212 -25.64 -5.35 3.39e+01 1eo6A 117 -25.28 -5.34 3.41e+01 1lu9A 287 -27.23 -5.34 3.41e+01 1add 349 -28.21 -5.33 3.44e+01 2cba 260 -26.98 -5.31 3.50e+01 1lk3A 160 -24.79 -5.28 3.57e+01 6prcL 273 -25.64 -5.28 3.59e+01 1gw0A 559 -28.29 -5.26 3.63e+01 1fxmA 302 -26.73 -5.26 3.64e+01 1k6aA 303 -26.73 -5.26 3.65e+01 1garA 212 -25.64 -5.26 3.65e+01 1gokA 303 -26.73 -5.25 3.66e+01 1dxrL 273 -25.64 -5.25 3.68e+01 1jkxA 212 -25.65 -5.24 3.69e+01 1h0xA 100 -26.95 -5.22 3.75e+01 3chbD 104 -23.89 -5.21 3.79e+01 1b3rA 431 -27.09 -5.20 3.81e+01 1fpxA 352 -28.68 -5.18 3.88e+01