% 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.YGR206W.t2k-100-30-str Host: cc57 Tue Nov 12 14:56:42 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR206W % --------------------------------------------------------------------- % 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 YGR206W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR206W.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 102 nodes, 68.78 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(=2.2897) * Reverse)^tau(=0.7908))) % 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 1octC 156 -29.30 -9.79 6.11e-02 1e3oC 160 -27.76 -8.37 2.38e-01 1au7A 146 -25.71 -7.34 6.62e-01 1oxa 403 -27.65 -7.05 8.82e-01 1eupA 403 -27.68 -6.97 9.57e-01 1jipA 403 -27.59 -6.85 1.08e+00 1d5yA 292 -28.58 -6.82 1.12e+00 1phk 298 -26.90 -6.77 1.18e+00 1hlrA 907 -29.20 -6.66 1.32e+00 1e3dB 542 -28.29 -6.47 1.60e+00 1ipaA 274 -25.37 -6.37 1.77e+00 1sesA 421 -27.01 -6.28 1.95e+00 1g9pA 45 -22.70 -6.15 2.23e+00 1pou 71 -25.08 -5.80 3.20e+00 1fvaA 217 -25.59 -5.69 3.61e+00 1g84A 105 -22.49 -5.60 3.99e+00 16vpA 366 -26.32 -5.52 4.33e+00 1ltdA 506 -28.18 -5.52 4.34e+00 1cr1A 296 -24.81 -5.49 4.48e+00 1cr0A 296 -24.80 -5.40 4.89e+00 1a7j 290 -25.33 -5.39 4.94e+00 1k4wA 252 -25.30 -5.34 5.24e+00 1cydA 244 -24.69 -5.26 5.69e+00 1qceA 123 -24.24 -5.21 6.04e+00 1sra 151 -25.08 -5.11 6.73e+00 1hueA 90 -21.89 -5.09 6.84e+00 1qlaB 239 -25.27 -5.07 7.02e+00 1aym3 238 -24.28 -5.04 7.25e+00 1bed 181 -23.68 -5.03 7.32e+00 6tmnE 316 -24.82 -4.96 7.87e+00 2tmnE 316 -24.83 -4.96 7.92e+00 1b8wA 42 -20.52 -4.95 7.94e+00 8tlnE 316 -24.82 -4.95 8.02e+00 1hyt 316 -24.82 -4.94 8.02e+00 1rh2F 165 -25.14 -4.94 8.06e+00 1ibsA 317 -24.39 -4.83 9.07e+00 1jf2A 195 -26.50 -4.80 9.35e+00 1e0cA 271 -24.20 -4.80 9.43e+00 1iqcA 308 -25.52 -4.78 9.56e+00 1fqjC 42 -20.04 -4.78 9.59e+00 1k3eA 156 -22.98 -4.73 1.02e+01 1gv4A 528 -25.50 -4.71 1.03e+01 1el4A 195 -25.81 -4.70 1.05e+01 1klqA 197 -23.31 -4.69 1.06e+01 1tif 78 -20.52 -4.66 1.10e+01 1ql0A 241 -23.80 -4.55 1.24e+01 1nubA 229 -25.33 -4.55 1.24e+01 1g8lA 411 -25.00 -4.51 1.29e+01 1smnA 245 -23.83 -4.51 1.30e+01 1qaeA 245 -23.83 -4.49 1.33e+01 1jy1A 464 -26.05 -4.48 1.34e+01 1g8tA 245 -23.82 -4.47 1.35e+01 1poiA 317 -24.20 -4.46 1.37e+01 1fcbA 511 -27.09 -4.41 1.44e+01 1dr9A 201 -22.22 -4.38 1.49e+01 1jjiA 311 -25.60 -4.34 1.56e+01 1go4A 205 -23.56 -4.29 1.64e+01 1qfcA 306 -23.65 -4.28 1.66e+01 1dkuA 317 -23.76 -4.26 1.71e+01 1drqA 131 -23.05 -4.21 1.80e+01 1pvc2 271 -23.91 -4.18 1.86e+01 1d06A 130 -21.93 -4.18 1.88e+01 1egdA 396 -24.51 -4.15 1.93e+01 1iioA 84 -21.21 -4.15 1.94e+01 1dkrA 317 -23.73 -4.14 1.95e+01 1ewnA 219 -22.95 -4.13 1.98e+01 1toaA 313 -23.98 -4.10 2.04e+01 1ibcB 88 -21.42 -4.07 2.13e+01 1hleA 345 -23.80 -4.06 2.14e+01 1kyqA 274 -24.04 -4.04 2.20e+01 1drmA 131 -22.65 -4.03 2.22e+01 1b6cB 342 -23.95 -4.02 2.23e+01 1e42A 258 -23.52 -3.99 2.32e+01 1qddA 144 -21.98 -3.98 2.34e+01 1cdb 105 -21.64 -3.93 2.48e+01 1ew0A 130 -22.02 -3.92 2.50e+01 1xwl 580 -25.86 -3.90 2.57e+01 1edg 380 -24.90 -3.89 2.59e+01 1hhnA 101 -21.25 -3.88 2.62e+01 2ucz 165 -23.13 -3.88 2.63e+01 1cixA 44 -19.38 -3.88 2.64e+01 1gya 105 -21.43 -3.87 2.65e+01 1hre 67 -20.58 -3.86 2.70e+01 1i1rB 181 -23.41 -3.85 2.73e+01 1t7pA 698 -26.14 -3.84 2.75e+01 1axh 37 -19.27 -3.83 2.77e+01 1m6iA 493 -24.15 -3.79 2.91e+01 1bmqB 88 -21.05 -3.76 3.02e+01 1hlgA 371 -23.91 -3.75 3.04e+01 1dujA 187 -22.40 -3.75 3.05e+01 1bbt1 213 -22.75 -3.75 3.05e+01 1qgjA 300 -23.89 -3.74 3.08e+01 1lit 144 -21.65 -3.69 3.26e+01 1a73A 163 -23.22 -3.69 3.27e+01 1i50C 318 -23.89 -3.68 3.31e+01 1vpsA 289 -23.36 -3.67 3.34e+01 1p35A 299 -23.48 -3.66 3.39e+01 5csmA 256 -23.46 -3.65 3.40e+01 2bc2A 227 -23.58 -3.65 3.43e+01 1qqp1 213 -22.71 -3.64 3.45e+01 1vjw 60 -20.06 -3.63 3.50e+01 1hae 63 -19.53 -3.60 3.60e+01 1dytA 133 -21.84 -3.59 3.68e+01 1huuA 90 -19.91 -3.58 3.69e+01 1csmA 256 -23.36 -3.57 3.74e+01 3bdpA 580 -25.55 -3.56 3.78e+01 1vpsB 289 -23.24 -3.56 3.80e+01 1hcl 298 -23.28 -3.52 3.96e+01 1d0iA 156 -21.73 -3.52 3.97e+01