% 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.YDL009C.t2k-100-30-dssp-ehl2 Host: cc55 Mon Nov 11 02:16:38 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YDL0/YDL009C % --------------------------------------------------------------------- % 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 YDL009C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YDL009C.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 108 nodes, 72.46 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(=2.2302) * Reverse)^tau(=0.7734))) % 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 1jffA 451 -29.35 -8.00 6.76e-01 1ton 235 -27.70 -7.50 1.06e+00 1gnyA 153 -25.75 -6.39 2.98e+00 1i0rA 169 -25.34 -6.04 4.17e+00 1i0sA 169 -25.34 -6.04 4.17e+00 1c0pA 363 -27.22 -5.95 4.55e+00 1jer 138 -23.74 -5.76 5.46e+00 1a7m 180 -24.54 -5.75 5.49e+00 2cbp 96 -23.02 -5.53 6.78e+00 1mi1A 414 -25.77 -5.48 7.16e+00 1ff9A 450 -26.45 -5.44 7.41e+00 1dhx 967 -28.97 -5.29 8.57e+00 1g6oA 330 -26.43 -5.28 8.69e+00 1kdxA 81 -21.41 -4.98 1.17e+01 1e9iA 431 -25.64 -4.86 1.32e+01 1bg2 325 -25.86 -4.85 1.33e+01 1k9jA 139 -23.51 -4.79 1.41e+01 1k8kE 178 -24.06 -4.68 1.57e+01 1l1oC 181 -23.63 -4.64 1.64e+01 1fj7A 101 -22.13 -4.62 1.69e+01 1ycqA 107 -21.64 -4.59 1.72e+01 1mpyA 307 -25.12 -4.53 1.83e+01 1a48 306 -24.64 -4.44 2.01e+01 1ast 200 -23.14 -4.44 2.02e+01 1iae 200 -23.14 -4.44 2.02e+01 1iab 200 -23.14 -4.43 2.05e+01 1k8vA 40 -19.44 -4.41 2.07e+01 1ik9C 37 -18.84 -4.39 2.12e+01 1fwp 139 -22.56 -4.34 2.24e+01 1ezvC 385 -28.91 -4.32 2.28e+01 1lki 180 -22.96 -4.28 2.38e+01 1rfa 79 -20.67 -4.24 2.47e+01 1k6dA 220 -23.42 -4.18 2.63e+01 1opaA 135 -23.22 -4.17 2.67e+01 1kq4A 232 -23.20 -4.17 2.67e+01 1hzxA 349 -25.87 -4.15 2.73e+01 1e8yA 966 -27.18 -4.13 2.77e+01 1opbA 135 -23.22 -4.13 2.79e+01 1fjeB 175 -22.66 -4.12 2.81e+01 1k8kD 300 -24.34 -4.09 2.91e+01 1gzqA 300 -25.97 -4.09 2.91e+01 1klo 162 -24.29 -4.04 3.04e+01 1b5fB 87 -21.44 -4.00 3.18e+01 1kyoC 385 -28.94 -3.98 3.24e+01 1qntA 176 -23.10 -3.98 3.26e+01 1bqbA 301 -23.98 -3.96 3.33e+01 1jg5A 83 -21.56 -3.93 3.44e+01 1is8K 84 -21.54 -3.90 3.54e+01 1ki1B 352 -24.19 -3.82 3.82e+01 1fl7B 111 -21.99 -3.81 3.88e+01 1i1rB 181 -23.50 -3.80 3.94e+01 1b2vA 188 -22.83 -3.78 3.99e+01 1dk0A 188 -22.83 -3.78 3.99e+01