% 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. % --------------------------------------------------------------------- % strfoo.1.YGR213C.t2k-100-30-str Host: cc65 Tue Nov 12 16:09:51 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR213C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.strs % % 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 YGR213C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR213C.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 318 nodes, 216.66 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(=2.2642) * Reverse)^tau(=0.7207))) % 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 1fqyA 269 -40.58 -11.57 1.97e-01 1jb0A 755 -45.00 -9.90 6.02e-01 1j4nA 271 -42.55 -9.32 9.00e-01 1dxrH 258 -32.83 -9.06 1.08e+00 6prcH 258 -32.73 -8.93 1.18e+00 1i37A 260 -32.53 -8.23 1.95e+00 1gkmA 509 -34.83 -8.04 2.23e+00 1eagA 342 -28.51 -7.46 3.41e+00 1qlaC 256 -41.09 -7.42 3.53e+00 1be3C 379 -43.17 -7.41 3.55e+00 1b8fA 509 -34.31 -7.39 3.59e+00 1ks9A 291 -31.62 -7.24 4.01e+00 1jfzA 154 -31.96 -6.90 5.19e+00 1dt6A 473 -32.61 -6.89 5.23e+00 1pdz 434 -31.53 -6.71 6.00e+00 1eia 207 -30.09 -6.69 6.10e+00 1fcyA 236 -32.71 -6.68 6.15e+00 1ithA 141 -29.00 -6.62 6.43e+00 2lbd 267 -33.11 -6.60 6.52e+00 1afrA 345 -33.30 -6.59 6.56e+00 1ldfA 281 -39.27 -6.54 6.83e+00 1fc6A 388 -28.14 -6.44 7.39e+00 4lbd 267 -32.92 -6.40 7.59e+00 1clqA 903 -33.27 -6.34 7.99e+00 1dofA 403 -34.74 -6.12 9.49e+00 1i4sA 147 -31.48 -6.11 9.55e+00 1ass 159 -25.65 -5.97 1.07e+01 1f1oA 431 -32.86 -5.89 1.14e+01 1vnc 609 -34.22 -5.88 1.14e+01 1aijL 281 -39.41 -5.86 1.16e+01 1fp1D 372 -29.27 -5.78 1.24e+01 1e2xA 243 -30.11 -5.77 1.25e+01 1a8h 500 -30.98 -5.77 1.25e+01 1hw1A 239 -30.44 -5.62 1.41e+01 1asx 159 -24.89 -5.53 1.51e+01 1eysH 259 -29.84 -5.44 1.62e+01 1fx8A 281 -37.99 -5.37 1.72e+01 1g8iA 190 -29.81 -5.33 1.78e+01 1vns 609 -33.20 -5.29 1.84e+01 1dl5A 317 -26.86 -5.28 1.85e+01 1io7A 368 -29.25 -5.18 2.01e+01 1ehkA 562 -43.15 -5.16 2.04e+01 1jpzA 473 -34.19 -5.15 2.06e+01 1ciy 590 -34.58 -5.13 2.09e+01 1aoa 275 -32.42 -5.13 2.09e+01 1bcfA 158 -31.80 -5.12 2.10e+01 1do0A 442 -28.71 -5.12 2.11e+01 1ireB 228 -28.31 -5.10 2.14e+01 2eiaB 206 -28.29 -5.08 2.18e+01 1ahxA 396 -27.85 -5.05 2.22e+01 1dxrM 323 -34.39 -5.02 2.29e+01 1noyA 388 -30.50 -4.99 2.34e+01 1bj4A 470 -28.01 -4.95 2.43e+01 1qisA 396 -27.94 -4.89 2.55e+01 1dklA 410 -30.12 -4.87 2.60e+01 1fpqA 372 -27.92 -4.87 2.60e+01 1uby 367 -32.70 -4.86 2.62e+01 1qpzA 340 -26.56 -4.83 2.69e+01 1wetA 340 -26.57 -4.81 2.73e+01 1yveJ 524 -32.09 -4.80 2.74e+01 1dkqA 410 -29.83 -4.79 2.77e+01 1kwsA 261 -25.41 -4.76 2.84e+01 1ghpA 258 -26.87 -4.75 2.86e+01 1fggA 261 -25.43 -4.74 2.88e+01 1dfoA 417 -28.22 -4.72 2.93e+01 1a7aA 432 -27.96 -4.66 3.09e+01 3ertA 261 -30.52 -4.61 3.22e+01 2hgsA 474 -27.10 -4.60 3.25e+01 1edoA 244 -27.02 -4.60 3.25e+01 2pgd 482 -31.59 -4.56 3.37e+01 1ocrC 261 -41.03 -4.55 3.39e+01 1f44A 324 -28.84 -4.55 3.39e+01 1qmgA 524 -31.81 -4.55 3.39e+01 1art 396 -27.32 -4.54 3.41e+01 1etu 394 -29.83 -4.51 3.51e+01 1gk4C 84 -26.80 -4.49 3.55e+01 1nozA 388 -29.33 -4.47 3.62e+01 1dbqA 289 -26.16 -4.46 3.67e+01 1ars 396 -26.99 -4.45 3.70e+01 2oneA 436 -29.46 -4.44 3.71e+01 1fdyA 297 -26.39 -4.44 3.73e+01 1crxA 322 -28.66 -4.40 3.85e+01 1ifa 158 -27.54 -4.40 3.86e+01 1iakA 199 -24.92 -4.39 3.88e+01 1hw5A 210 -26.30 -4.36 3.97e+01 1spa 396 -26.96 -4.36 3.99e+01