% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 09/03/03_16:30:36 % (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-T2K, 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, et al., What is the value added by human intervention in protein % structure prediction, Proteins: Stucture, Function, Genetics 45(S5):86--91, 2001. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YGR212W.t2k-100-30-dssp-ehl2 Host: cc50 Sun Oct 12 01:25:39 2003 % 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.dssps % % 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.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8763 sequences, 2072585 residues, 469 nodes, 427.12 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 (=8162) sequences: % N / (1 + exp(-(lambda(=1.5021) * Reverse)^tau(=0.7864))) % 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 -34.45 -11.00 9.34e-01 8pchA 220 -30.85 -9.44 2.61e+00 1i19A 561 -33.93 -9.08 3.32e+00 1fljA 260 -31.49 -8.48 4.99e+00 1uc8A 280 -30.23 -7.73 8.43e+00 1azo 232 -29.54 -7.67 8.80e+00 1ipaA 274 -29.64 -7.38 1.08e+01 1bgp 309 -29.54 -7.23 1.19e+01 1amj 754 -32.80 -7.23 1.19e+01 8acn 754 -32.80 -7.20 1.22e+01 1gk8A 475 -31.34 -7.09 1.32e+01 1oe4A 247 -30.08 -6.90 1.51e+01 1el6A 219 -30.47 -6.88 1.53e+01 1keiA 316 -29.32 -6.73 1.71e+01 1g4uS 383 -31.40 -6.68 1.77e+01 1hyt 316 -29.19 -6.64 1.82e+01 6tmnE 316 -29.19 -6.64 1.82e+01 8tlnE 316 -29.19 -6.64 1.82e+01 1el6B 219 -30.49 -6.64 1.82e+01 1g4wR 383 -31.80 -6.63 1.84e+01 2tmnE 316 -29.19 -6.62 1.84e+01 1lnsA 763 -32.25 -6.58 1.90e+01 1b0jA 754 -33.00 -6.56 1.93e+01 1dmuA 299 -29.80 -6.56 1.93e+01 1cxqA 162 -28.09 -6.56 1.94e+01 6acn 754 -32.45 -6.42 2.14e+01 1c96A 753 -32.39 -6.39 2.18e+01 7acn 754 -32.43 -6.38 2.19e+01 2minB 522 -31.10 -6.35 2.25e+01 1bk1 184 -28.68 -6.32 2.29e+01 1jvpP 298 -30.91 -6.32 2.30e+01 1f5mB 180 -29.25 -6.25 2.42e+01 1f5mA 180 -29.25 -6.25 2.42e+01 1mkiA 330 -30.05 -6.22 2.48e+01 1a3c 181 -31.16 -6.21 2.48e+01 1vsd 152 -28.01 -6.21 2.50e+01 1gpb 842 -32.18 -6.19 2.52e+01 1asu 162 -28.06 -6.18 2.54e+01 1c8kA 842 -32.20 -6.12 2.65e+01 1pda 315 -28.38 -6.10 2.70e+01 1a8i 842 -32.20 -6.09 2.71e+01 1h5uA 842 -32.19 -6.09 2.72e+01 1a15A 67 -25.57 -6.07 2.76e+01 1hcl 298 -30.53 -6.05 2.81e+01 1qo7A 394 -29.48 -5.97 2.97e+01 1gtkA 313 -28.31 -5.96 3.00e+01 1n99A 166 -27.60 -5.96 3.00e+01 1qniA 581 -31.48 -5.94 3.04e+01 1f4qA 165 -27.03 -5.83 3.30e+01 1h2aL 567 -29.88 -5.82 3.32e+01 1e1xA 299 -30.24 -5.82 3.32e+01 1gz8A 299 -30.24 -5.80 3.38e+01 1k94A 165 -27.19 -5.78 3.43e+01 1j7iA 264 -29.97 -5.74 3.51e+01 1j7lA 264 -29.74 -5.64 3.78e+01 2fnbA 95 -28.14 -5.64 3.79e+01