% 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.YGR235C.t2k-100-30-dssp-ehl2 Host: cc86 Tue Nov 12 19:06:53 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.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 YGR235C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR235C.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 234 nodes, 156.59 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(=1.7891) * Reverse)^tau(=0.7754))) % 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 1jetA 517 -36.11 -12.95 7.90e-02 1jevA 517 -36.11 -12.93 7.99e-02 2olbA 517 -35.69 -12.60 1.01e-01 1iq0A 592 -34.45 -11.64 1.95e-01 1sig 339 -34.27 -10.93 3.24e-01 1iwhB 146 -31.30 -10.59 4.12e-01 1fliA 98 -27.93 -8.94 1.37e+00 1ass 159 -29.95 -8.30 2.21e+00 1asx 159 -29.29 -8.14 2.51e+00 1g0u1 266 -30.24 -7.67 3.59e+00 1ryp2 233 -29.78 -7.40 4.42e+00 2ctb 307 -28.56 -7.18 5.24e+00 1yme 309 -28.36 -7.01 6.00e+00 1j54A 186 -27.43 -6.93 6.36e+00 1necA 216 -29.24 -6.56 8.56e+00 1kl7A 514 -30.71 -6.53 8.79e+00 1j5eC 239 -27.04 -6.38 9.88e+00 1dxtB 147 -28.90 -6.34 1.02e+01 1babB 146 -28.88 -6.33 1.03e+01 1fjgC 239 -26.68 -6.28 1.07e+01 2ctc 307 -27.67 -6.24 1.11e+01 1nksA 194 -25.98 -5.99 1.35e+01 1gd5A 130 -26.44 -5.98 1.36e+01 1irdB 146 -27.46 -5.96 1.39e+01 1hcnA 92 -24.11 -5.92 1.44e+01 1im4A 221 -26.65 -5.91 1.44e+01 6cpa 307 -27.05 -5.91 1.45e+01 1eny 268 -27.16 -5.82 1.55e+01 1dz7A 92 -23.82 -5.82 1.56e+01 1zid 268 -27.16 -5.80 1.58e+01 1fhjB 146 -28.31 -5.63 1.82e+01 1blu 82 -23.41 -5.61 1.85e+01 1ib8A 164 -25.48 -5.60 1.86e+01 1ci8A 392 -27.64 -5.59 1.88e+01 1ci9A 392 -27.64 -5.51 2.01e+01 1udh 244 -26.82 -5.45 2.11e+01 1ajsA 412 -28.61 -5.45 2.12e+01 1udg 244 -26.78 -5.40 2.19e+01 2spcA 107 -26.92 -5.38 2.24e+01 1fjgR 88 -24.27 -5.33 2.32e+01 1amuA 563 -27.79 -5.26 2.47e+01 1ax8 146 -26.26 -5.24 2.51e+01 1g8yA 279 -27.02 -5.22 2.57e+01 1eupA 403 -31.40 -5.19 2.61e+01 1mgtA 174 -26.67 -5.16 2.69e+01 1bob 320 -27.11 -5.15 2.70e+01 1cot 129 -24.33 -5.14 2.73e+01 1cem 363 -27.41 -5.14 2.73e+01 1kwfA 363 -27.43 -5.14 2.73e+01 1spgB 147 -26.67 -5.13 2.76e+01 1lucB 324 -27.34 -5.10 2.82e+01 1oxa 403 -31.27 -5.07 2.89e+01 1dhs 344 -27.89 -5.03 3.00e+01 1cyo 93 -22.77 -4.99 3.11e+01 1icrA 217 -26.87 -4.95 3.22e+01 1lqxA 82 -22.42 -4.95 3.22e+01 1c3wA 222 -26.82 -4.92 3.29e+01 1e69B 322 -28.86 -4.87 3.44e+01 1amk 251 -27.15 -4.86 3.45e+01 1k2yX 463 -28.23 -4.83 3.56e+01 1kewA 361 -26.94 -4.82 3.57e+01 1g4mA 393 -26.08 -4.82 3.59e+01 1jkfA 533 -27.73 -4.81 3.62e+01 1lfpA 249 -26.26 -4.79 3.69e+01 1jkiA 533 -27.68 -4.78 3.69e+01 1a99A 344 -26.43 -4.78 3.72e+01 1jenA 267 -26.52 -4.77 3.74e+01 1reqB 637 -29.18 -4.77 3.75e+01 1k8kA 418 -28.14 -4.74 3.83e+01 1g7dA 106 -26.40 -4.71 3.93e+01