% 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. % --------------------------------------------------------------------- % alphafoo.1.YDR525W.t2k-100-30-alpha Host: cc34 Sat Dec 7 04:40:58 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YDR5/YDR525W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.alphas % % 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 YDR525W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YDR525W.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7458 sequences, 1753770 residues, 110 nodes, 75.19 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(=2.6381) * Reverse)^tau(=0.7382))) % 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 1ocrC 261 -28.56 -8.04 5.31e-01 2occC 261 -28.57 -8.03 5.36e-01 1ev7B 317 -27.10 -7.33 9.95e-01 1ev7A 317 -26.71 -6.94 1.41e+00 1a88A 275 -26.84 -6.79 1.62e+00 1iawA 317 -26.11 -6.18 2.85e+00 1eb7A 323 -25.92 -5.82 4.02e+00 1f28A 297 -25.94 -5.39 6.07e+00 1brlB 324 -25.37 -5.36 6.22e+00 1lucB 324 -25.28 -5.28 6.76e+00 5csmA 256 -24.32 -5.08 8.22e+00 1csmA 256 -24.34 -5.06 8.40e+00 1ap6A 198 -24.18 -5.03 8.59e+00 1hxmA 229 -25.31 -5.02 8.68e+00 1abmA 198 -24.14 -4.98 9.07e+00 1fj7A 101 -22.76 -4.95 9.35e+00 1fjeB 175 -23.34 -4.78 1.10e+01 1n0nA 199 -23.91 -4.74 1.15e+01 1a6wH 120 -22.94 -4.65 1.26e+01 1avmA 201 -24.11 -4.58 1.35e+01 1a8s 273 -24.08 -4.58 1.35e+01 1cto 109 -21.78 -4.53 1.43e+01 1b8fA 509 -26.66 -4.39 1.64e+01 1fzaB 328 -24.83 -4.34 1.73e+01 1fgyA 127 -21.98 -4.33 1.73e+01 1gkmA 509 -26.56 -4.31 1.78e+01 2xat 212 -24.25 -4.29 1.82e+01 1pex 207 -23.77 -4.27 1.86e+01 1bsmA 201 -23.67 -4.23 1.92e+01 1mn1 357 -25.16 -4.23 1.94e+01 1b2pA 119 -22.15 -4.23 1.94e+01 1kkcA 221 -22.90 -4.18 2.03e+01 1ihfB 94 -21.30 -4.18 2.04e+01 1xat 212 -24.06 -4.17 2.05e+01 2pna 104 -21.35 -4.16 2.08e+01 1mlcB 218 -24.14 -4.12 2.17e+01 1f60A 458 -25.13 -4.06 2.30e+01 1iu4A 331 -24.40 -4.00 2.44e+01 1mgsA 73 -20.75 -4.00 2.45e+01 2occB 227 -25.23 -3.97 2.53e+01 1dfnA 30 -18.51 -3.94 2.62e+01 1jiwI 106 -21.89 -3.89 2.75e+01 1ec7A 446 -25.22 -3.86 2.84e+01 1d5nA 205 -22.64 -3.83 2.92e+01 1kp0A 402 -24.81 -3.78 3.11e+01 1fjjA 159 -22.40 -3.77 3.13e+01 1gcf 109 -21.24 -3.70 3.36e+01 1lnh 857 -26.67 -3.70 3.37e+01 1tyfA 193 -22.30 -3.68 3.44e+01 1d0bA 213 -22.11 -3.68 3.44e+01 1ftrA 296 -23.33 -3.67 3.48e+01 1pdgC 109 -20.69 -3.64 3.59e+01 1i0hA 205 -22.43 -3.64 3.61e+01 4htcI 65 -21.24 -3.61 3.72e+01 1hm5A 558 -25.21 -3.60 3.75e+01 1jtdB 273 -23.36 -3.60 3.76e+01 1c5cH 215 -23.21 -3.59 3.79e+01