% 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. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YGR035C.t2k-100-30-dssp-ehl2 Host: cc41 Fri Nov 8 19:04:14 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR035C % --------------------------------------------------------------------- % 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 YGR035C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR035C.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 117 nodes, 78.17 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(=2.5060) * Reverse)^tau(=0.7193))) % 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 1l2rA 458 -31.12 -8.30 1.03e+00 1l2qA 458 -31.12 -8.29 1.03e+00 1c4xA 285 -28.55 -8.27 1.05e+00 1a3gA 308 -27.99 -7.98 1.31e+00 1i1kA 309 -27.42 -7.46 1.97e+00 1gtzA 156 -25.20 -6.67 3.73e+00 1d0iA 156 -25.24 -6.67 3.74e+00 1hlrA 907 -29.52 -6.61 3.91e+00 1lba 146 -25.67 -6.29 5.09e+00 1qc5A 192 -25.32 -6.29 5.10e+00 1oya 400 -27.64 -6.12 5.85e+00 1kqfC 217 -26.50 -5.94 6.85e+00 1bxkA 355 -27.55 -5.91 7.00e+00 1oyb 400 -27.45 -5.85 7.40e+00 1noyA 388 -27.15 -5.82 7.56e+00 1c4zA 358 -26.59 -5.74 8.12e+00 1jjiA 311 -26.22 -5.72 8.24e+00 1jqgA 433 -26.71 -5.46 1.03e+01 1jmoA 480 -28.30 -5.44 1.05e+01 1dhpA 292 -25.66 -5.42 1.06e+01 1ggvA 232 -25.76 -5.30 1.18e+01 1oyc 400 -26.72 -5.27 1.21e+01 1hllA 32 -19.97 -5.15 1.35e+01 1ako 268 -25.04 -5.14 1.36e+01 1l5jA 865 -29.10 -5.10 1.41e+01 1d8cA 723 -28.45 -5.07 1.45e+01 1inlA 296 -25.35 -5.02 1.52e+01 1jq3A 296 -25.36 -4.99 1.55e+01 1qasA 622 -27.70 -4.97 1.59e+01 3dfr 162 -23.47 -4.91 1.66e+01 1qatB 622 -27.73 -4.87 1.73e+01 1lxtA 561 -27.45 -4.80 1.84e+01 1djxA 624 -27.70 -4.80 1.84e+01 1djxB 624 -27.72 -4.76 1.91e+01 1xnb 185 -22.96 -4.69 2.04e+01 1bpv 112 -22.08 -4.68 2.04e+01 1qe3A 489 -26.54 -4.68 2.05e+01 1jy5A 212 -24.43 -4.66 2.09e+01 1vtp 26 -18.37 -4.60 2.20e+01 1epxA 370 -25.53 -4.51 2.39e+01 1e9kA 38 -19.49 -4.50 2.40e+01 1ao8 162 -23.23 -4.49 2.44e+01 1nozA 388 -25.77 -4.46 2.49e+01 1hizA 379 -26.42 -4.43 2.57e+01 1im8A 244 -24.51 -4.42 2.59e+01 1ayx 492 -26.37 -4.42 2.59e+01 1g73A 162 -22.68 -4.42 2.60e+01 1wad 112 -21.96 -4.38 2.69e+01 1kewA 361 -25.76 -4.37 2.72e+01 1jyaA 130 -24.00 -4.30 2.88e+01 1k8kD 300 -28.99 -4.27 2.98e+01 1di0A 158 -23.03 -4.25 3.04e+01 3pmgA 561 -26.84 -4.19 3.19e+01 1din 236 -25.40 -4.12 3.42e+01 1cb0A 283 -26.50 -4.12 3.43e+01 1qhtA 775 -27.48 -4.11 3.46e+01 1ecpA 238 -23.88 -4.03 3.71e+01 1cs1C 386 -24.64 -4.00 3.81e+01 1rmd 116 -22.66 -4.00 3.83e+01 1k4wA 252 -24.69 -3.98 3.90e+01