% 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.YGR025W.t2k-100-30-dssp-ehl2 Host: cc47 Fri Nov 8 17:47:35 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR025W % --------------------------------------------------------------------- % 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 YGR025W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR025W.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7310 sequences, 1706072 residues, 101 nodes, 67.37 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(=2.2939) * Reverse)^tau(=0.7513))) % 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 1slvA 142 -28.09 -7.39 1.66e+00 1sluA 142 -27.97 -7.05 2.23e+00 1ihgA 370 -28.70 -6.84 2.67e+00 1i2hA 168 -26.61 -6.78 2.81e+00 1irk 306 -26.18 -6.43 3.85e+00 1ir3A 306 -26.19 -6.39 3.99e+00 1jroB 777 -28.83 -6.20 4.72e+00 1jpaA 312 -26.44 -6.20 4.72e+00 1mak 113 -24.66 -6.05 5.39e+00 1ddvA 111 -25.37 -6.02 5.53e+00 1ddwA 120 -25.31 -5.98 5.70e+00 1jenA 267 -27.27 -5.94 5.92e+00 1f0lA 535 -27.18 -5.93 5.99e+00 1apyB 141 -24.03 -5.90 6.16e+00 1ddt 535 -27.12 -5.89 6.18e+00 1dfnA 30 -21.80 -5.78 6.82e+00 1eaiC 61 -24.25 -5.41 9.57e+00 1j6nA 303 -24.39 -5.20 1.17e+01 1avgI 142 -25.77 -5.02 1.38e+01 1je5A 206 -25.61 -4.96 1.45e+01 1ib8A 164 -24.18 -4.91 1.54e+01 1lba 146 -23.36 -4.82 1.67e+01 1qr6A 584 -25.92 -4.79 1.72e+01 1iqaA 160 -24.13 -4.70 1.86e+01 1rhd 293 -24.32 -4.69 1.88e+01 1fthA 122 -22.14 -4.59 2.08e+01 1dlfL 113 -23.11 -4.55 2.15e+01 1a1z 91 -20.23 -4.50 2.27e+01 1a4yB 123 -23.47 -4.45 2.38e+01 1cp3A 277 -25.00 -4.41 2.46e+01 1rhs 296 -24.01 -4.37 2.55e+01 1g0sA 209 -24.79 -4.35 2.61e+01 1qppA 218 -25.50 -4.30 2.74e+01 1qhxA 178 -22.48 -4.29 2.77e+01 1pdgA 109 -26.42 -4.28 2.80e+01 1pdgC 109 -25.59 -4.27 2.83e+01 1nglA 179 -26.09 -4.27 2.83e+01 1ecl 597 -25.77 -4.27 2.83e+01 1icfA 175 -24.28 -4.21 2.98e+01 1b65A 375 -25.12 -4.18 3.07e+01 1ftkA 279 -24.08 -4.14 3.20e+01 1gr2A 279 -24.09 -4.14 3.21e+01 1hxmA 229 -25.96 -4.12 3.27e+01 1qhsA 178 -22.22 -4.03 3.56e+01 1nra 63 -21.24 -3.99 3.71e+01 1kyqA 274 -23.46 -3.96 3.81e+01 1dqsA 393 -24.46 -3.96 3.82e+01 1jm7B 117 -22.14 -3.93 3.93e+01