% 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. % --------------------------------------------------------------------- % stridefoo.1.YGR235C.t2k-100-30-stride-ebghtl Host: cc86 Tue Nov 12 18:56:22 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.2ds % % 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.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 234 nodes, 156.83 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(=1.7286) * Reverse)^tau(=0.7585))) % 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 -36.78 -14.13 9.14e-02 2olbA 517 -37.09 -13.99 9.97e-02 1jevA 517 -37.10 -13.96 1.02e-01 1jetA 517 -36.94 -13.81 1.12e-01 1iwhB 146 -34.15 -13.05 1.77e-01 1sig 339 -34.73 -11.10 6.05e-01 1fliA 98 -28.29 -9.24 2.05e+00 1ass 159 -29.60 -8.11 4.43e+00 1asx 159 -29.58 -7.99 4.81e+00 1eupA 403 -33.07 -7.76 5.65e+00 1nksA 194 -27.58 -7.75 5.69e+00 1babB 146 -28.91 -7.70 5.89e+00 1dxtB 147 -28.93 -7.70 5.90e+00 1fjgC 239 -28.00 -7.63 6.21e+00 1irdB 146 -28.78 -7.37 7.41e+00 1a6dA 545 -33.77 -7.20 8.42e+00 1cem 363 -29.29 -7.03 9.46e+00 1ci9A 392 -29.08 -6.99 9.75e+00 1fhjB 146 -30.28 -6.89 1.05e+01 1spgB 147 -28.27 -6.72 1.19e+01 1cyo 93 -24.47 -6.69 1.21e+01 1j54A 186 -27.51 -6.66 1.23e+01 1hcnA 92 -24.18 -6.66 1.24e+01 1amuA 563 -29.05 -6.59 1.31e+01 1oxa 403 -31.62 -6.52 1.37e+01 1jx4A 352 -31.05 -6.49 1.41e+01 1kwfA 363 -29.32 -6.33 1.58e+01 1ajsA 412 -29.46 -6.27 1.65e+01 1kl7A 514 -30.43 -6.05 1.93e+01 1ci8A 392 -28.12 -6.05 1.94e+01 1aisB 200 -27.01 -5.94 2.11e+01 1aep 161 -28.72 -5.88 2.20e+01 1im4A 221 -26.81 -5.88 2.20e+01 1k2yX 463 -28.93 -5.75 2.42e+01 1lqxA 82 -23.37 -5.71 2.50e+01 1i3dA 146 -28.54 -5.69 2.53e+01 1udg 244 -26.92 -5.68 2.55e+01 2spcA 107 -27.29 -5.67 2.57e+01 1epuA 591 -30.72 -5.67 2.57e+01 1udh 244 -26.90 -5.67 2.58e+01 1k8kA 418 -29.85 -5.66 2.59e+01 1necA 216 -27.92 -5.47 2.99e+01 1zid 268 -26.74 -5.45 3.04e+01 3pghA 587 -28.82 -5.41 3.12e+01 1kyoC 385 -29.38 -5.41 3.13e+01 1ll1 590 -29.95 -5.40 3.16e+01 1g4mA 393 -26.22 -5.39 3.19e+01 1jenA 267 -25.81 -5.37 3.22e+01 1cot 129 -24.26 -5.37 3.23e+01 1ezvC 385 -29.33 -5.35 3.28e+01 1avaA 403 -27.21 -5.34 3.30e+01 1a99A 344 -27.04 -5.28 3.46e+01 1dz7A 92 -23.12 -5.25 3.53e+01 1mgtA 174 -26.48 -5.23 3.60e+01 1jkiA 533 -28.09 -5.15 3.82e+01