% 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.YCL046W.t2k-100-30-alpha Host: cc66 Fri Dec 6 11:05:29 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YCL0/YCL046W % --------------------------------------------------------------------- % 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 YCL046W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YCL046W.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7458 sequences, 1753770 residues, 108 nodes, 74.02 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(=2.3744) * Reverse)^tau(=0.7743))) % 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 1eylA 186 -24.84 -6.33 2.10e+00 1gh6A 114 -23.96 -6.26 2.25e+00 1dd9A 338 -25.49 -5.69 4.04e+00 1j5eK 129 -23.41 -5.65 4.17e+00 2e2c 156 -23.65 -5.63 4.28e+00 1ghsA 306 -25.79 -5.58 4.48e+00 1bj8 109 -22.70 -5.45 5.16e+00 1havA 217 -24.74 -5.31 5.94e+00 1hxs3 237 -24.39 -5.17 6.86e+00 1dapA 320 -25.44 -5.04 7.87e+00 1ddeA 338 -24.87 -5.04 7.91e+00 1qa7A 217 -24.32 -4.95 8.69e+00 3dapA 320 -25.41 -4.91 9.05e+00 1h9oA 112 -22.67 -4.82 9.92e+00 1kijA 390 -25.42 -4.74 1.08e+01 1pgtA 210 -24.16 -4.73 1.09e+01 1g7fA 298 -24.99 -4.71 1.12e+01 1f06A 320 -25.11 -4.71 1.12e+01 1fjgK 129 -22.37 -4.64 1.21e+01 1qatB 622 -26.39 -4.60 1.26e+01 1qasA 622 -26.33 -4.56 1.31e+01 1i36A 264 -25.19 -4.51 1.38e+01 1lywA 97 -22.06 -4.51 1.38e+01 2tnfA 156 -23.48 -4.48 1.43e+01 1eqnA 321 -24.39 -4.44 1.49e+01 2hnp 321 -24.90 -4.44 1.49e+01 1bmv2 374 -25.27 -4.43 1.51e+01 1dbdA 100 -23.07 -4.40 1.56e+01 1djxA 624 -26.10 -4.36 1.62e+01 1lybA 97 -22.04 -4.35 1.64e+01 2fcr 173 -24.27 -4.34 1.66e+01 1elvA 333 -24.32 -4.33 1.67e+01 2omf 340 -24.95 -4.31 1.71e+01 1l0bA 229 -24.83 -4.31 1.72e+01 1qadA 111 -22.04 -4.30 1.74e+01 1gsoA 431 -25.00 -4.29 1.74e+01 1gg3A 279 -24.23 -4.29 1.75e+01 1dvfD 120 -21.88 -4.29 1.75e+01 1a0sP 413 -24.93 -4.26 1.81e+01 1kwsA 261 -24.50 -4.24 1.85e+01 1pauA 147 -23.84 -4.24 1.85e+01 1a0tP 413 -24.89 -4.23 1.87e+01 1id1A 153 -22.19 -4.14 2.06e+01 4eugA 229 -23.56 -4.12 2.12e+01 1avmA 201 -22.47 -4.10 2.17e+01 1kd6A 179 -23.85 -4.10 2.17e+01 1j5yA 187 -23.11 -4.06 2.25e+01 3eugA 229 -23.44 -4.05 2.29e+01 1rdr 461 -25.36 -4.04 2.31e+01 1qa7B 217 -23.74 -4.02 2.35e+01 1ek4A 418 -24.46 -4.02 2.37e+01 1djxB 624 -25.73 -3.98 2.45e+01 1m5dA 263 -23.31 -3.98 2.46e+01 1kshB 152 -21.96 -3.97 2.48e+01 1aym3 238 -23.02 -3.95 2.53e+01 1bsmA 201 -22.28 -3.95 2.53e+01 1ivzA 132 -21.50 -3.95 2.54e+01 1arb 268 -23.91 -3.93 2.60e+01 1ftkA 279 -23.52 -3.92 2.63e+01 1dd8A 406 -24.30 -3.91 2.65e+01 1m5eA 263 -23.18 -3.88 2.74e+01 1iml 76 -20.84 -3.87 2.77e+01 1gr2A 279 -23.49 -3.86 2.82e+01 1hm5A 558 -26.04 -3.82 2.93e+01 1bquA 215 -22.63 -3.81 2.95e+01 1fggA 261 -24.10 -3.80 3.01e+01 1dqrA 557 -26.06 -3.77 3.11e+01 1a76 326 -23.65 -3.76 3.12e+01 1cds 77 -20.44 -3.73 3.24e+01 1cdq 77 -20.38 -3.73 3.27e+01 1buyA 166 -22.22 -3.71 3.33e+01 1c3oB 382 -23.84 -3.68 3.42e+01 1euoA 180 -22.49 -3.68 3.43e+01 1hxxA 340 -24.26 -3.65 3.57e+01 1necA 216 -22.30 -3.63 3.63e+01 1stfI 98 -20.85 -3.59 3.82e+01 1cs0B 382 -23.66 -3.56 3.93e+01 1a9xB 379 -23.70 -3.56 3.94e+01 2kinB 100 -21.50 -3.55 3.97e+01 1jw3A 140 -21.48 -3.55 3.97e+01 1f35A 162 -22.04 -3.55 3.99e+01