% 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.YGR212W.t2k-100-30-str Host: cc46 Tue Nov 12 16:14:54 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR212W % --------------------------------------------------------------------- % 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 YGR212W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR212W.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 469 nodes, 317.12 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(=1.5692) * Reverse)^tau(=0.7601))) % 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 1l5aA 436 -37.88 -13.74 2.41e-01 1i19A 561 -35.58 -10.66 1.48e+00 1a15A 67 -30.33 -10.53 1.60e+00 1azo 232 -32.94 -10.47 1.65e+00 1h2aL 567 -34.46 -9.37 3.26e+00 1qg7A 67 -30.07 -9.37 3.26e+00 1dmuA 299 -33.03 -9.33 3.34e+00 1bgp 309 -31.81 -8.82 4.60e+00 6tmnE 316 -31.86 -8.66 5.11e+00 2tmnE 316 -31.86 -8.65 5.14e+00 1hyt 316 -31.86 -8.65 5.15e+00 8tlnE 316 -31.86 -8.65 5.16e+00 8acn 754 -34.10 -8.60 5.30e+00 8pchA 220 -30.68 -8.60 5.30e+00 1amj 754 -34.10 -8.59 5.34e+00 1e3dB 542 -33.03 -8.59 5.34e+00 1el6B 219 -31.56 -8.38 6.11e+00 1el6A 219 -31.43 -8.31 6.39e+00 1bk1 184 -30.89 -8.26 6.61e+00 1qusA 322 -31.37 -8.12 7.22e+00 1ltm 320 -31.25 -8.06 7.51e+00 1b0jA 754 -33.81 -8.00 7.82e+00 1c96A 753 -33.88 -7.75 9.21e+00 6acn 754 -33.76 -7.62 1.00e+01 7acn 754 -33.79 -7.55 1.05e+01 1icxA 155 -32.55 -7.54 1.06e+01 1ipaA 274 -29.13 -7.40 1.16e+01 1fa0B 537 -32.79 -7.35 1.19e+01 1gk8A 475 -30.79 -7.33 1.21e+01 1parA 53 -25.99 -7.30 1.23e+01 1gsoA 431 -32.62 -7.27 1.26e+01 1f1sA 814 -34.75 -7.24 1.29e+01 1dryA 324 -29.25 -7.15 1.37e+01 1bdtA 53 -25.70 -7.06 1.45e+01 1ds1A 324 -29.24 -7.04 1.47e+01 1eaxA 241 -30.17 -6.84 1.68e+01 1mykA 53 -25.54 -6.83 1.69e+01 1cv2A 296 -28.86 -6.82 1.70e+01 1drtA 324 -28.83 -6.76 1.77e+01 1fzyA 149 -29.43 -6.69 1.85e+01 1dkxA 219 -31.35 -6.64 1.92e+01 1f5mB 180 -30.07 -6.60 1.97e+01 1f5mA 180 -30.08 -6.58 2.00e+01 1jhnA 424 -32.09 -6.58 2.00e+01 1cxqA 162 -27.82 -6.55 2.05e+01 1ayx 492 -31.15 -6.44 2.20e+01 2fnbA 95 -29.66 -6.43 2.21e+01 1ffyA 917 -33.59 -6.37 2.31e+01 1qu2A 917 -33.59 -6.37 2.31e+01 1vsd 152 -27.71 -6.37 2.32e+01 1bazA 53 -25.08 -6.34 2.36e+01 1poc 134 -26.95 -6.32 2.39e+01 1h2rL 534 -33.07 -6.31 2.41e+01 1yer 228 -29.35 -6.31 2.41e+01 1jkgA 140 -28.18 -6.30 2.43e+01 1asu 162 -27.85 -6.30 2.43e+01 1qh0A 295 -30.02 -6.22 2.56e+01 1go2A 304 -30.06 -6.19 2.61e+01 1a3c 181 -29.03 -6.18 2.63e+01 1a6wL 109 -27.02 -6.14 2.70e+01 1prxA 224 -27.62 -6.10 2.78e+01 1dkzA 219 -31.28 -6.09 2.79e+01 1b2rA 304 -30.00 -6.08 2.82e+01 1a6uL 108 -26.72 -6.04 2.89e+01 1k94A 165 -28.00 -6.03 2.93e+01 1m22A 503 -29.96 -6.02 2.94e+01 1wwbX 103 -27.28 -6.01 2.97e+01 1que 303 -29.63 -6.00 2.98e+01 1bpr 191 -28.68 -6.00 2.99e+01 1aol 228 -28.13 -5.98 3.03e+01 1fa0A 537 -31.77 -5.97 3.04e+01 1jvpP 298 -30.86 -5.97 3.06e+01 1f4qA 165 -27.76 -5.92 3.14e+01 1h3nA 878 -32.40 -5.92 3.15e+01 1fv0A 121 -26.30 -5.80 3.42e+01 1kpmA 121 -26.29 -5.76 3.52e+01 1hcl 298 -30.64 -5.74 3.57e+01 1jn5A 140 -27.58 -5.74 3.59e+01 4xiaA 393 -28.49 -5.70 3.68e+01 7icd 416 -29.43 -5.61 3.91e+01