% 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.YEL014C.t2k-100-30-dssp-ehl2 Host: cc64 Sat Dec 7 07:08:59 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YEL0/YEL014C % --------------------------------------------------------------------- % 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 YEL014C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YEL014C.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7458 sequences, 1753770 residues, 102 nodes, 69.82 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(=2.2124) * Reverse)^tau(=0.7657))) % 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 1c8oA 300 -28.01 -7.18 1.80e+00 1eur 365 -28.81 -6.98 2.15e+00 1f0cA 305 -28.17 -6.88 2.35e+00 1hlcA 129 -27.40 -6.70 2.77e+00 1d6mA 653 -27.66 -6.30 3.99e+00 830cA 168 -25.94 -6.22 4.27e+00 1i7dA 659 -27.64 -6.19 4.40e+00 1ky9B 448 -27.99 -6.17 4.47e+00 1cxvA 164 -25.38 -6.04 5.04e+00 1ky9A 448 -27.96 -5.71 6.88e+00 4htcI 65 -22.89 -5.68 7.04e+00 1qhdA 398 -27.24 -5.66 7.20e+00 2bc2B 227 -25.87 -5.54 8.06e+00 2bc2A 227 -25.87 -5.46 8.63e+00 1h4wA 224 -26.72 -5.33 9.78e+00 1eut 605 -29.56 -5.11 1.21e+01 1k24A 253 -27.94 -4.96 1.40e+01 1euu 605 -29.56 -4.95 1.41e+01 1e7uA 961 -27.82 -4.76 1.70e+01 1qfxA 460 -27.73 -4.74 1.73e+01 1k5jA 124 -25.10 -4.63 1.92e+01 1tiu 98 -23.35 -4.59 2.00e+01 1k92A 455 -25.16 -4.58 2.01e+01 1idaA 99 -24.39 -4.58 2.02e+01 1fhoA 119 -25.13 -4.48 2.23e+01 1b8xA 280 -24.19 -4.47 2.25e+01 1bwyA 132 -24.41 -4.34 2.57e+01 1tit 98 -23.55 -4.30 2.66e+01 2bpa2 175 -24.83 -4.24 2.84e+01 4bcl 366 -26.64 -4.23 2.87e+01 1lci 550 -27.07 -4.22 2.89e+01 1h6fA 193 -24.51 -4.19 2.98e+01 1bak 119 -22.57 -4.18 3.02e+01 1aocA 175 -23.64 -4.17 3.04e+01 2eifA 136 -25.76 -4.15 3.10e+01 1dcjA 81 -20.57 -4.10 3.27e+01 1bvqA 141 -23.13 -4.08 3.34e+01 1lo7A 141 -23.36 -4.07 3.36e+01 1al0G 175 -24.24 -3.99 3.64e+01 1ei5A 520 -27.61 -3.95 3.81e+01 1bet 107 -22.61 -3.95 3.81e+01 1f97A 212 -25.19 -3.94 3.83e+01 1dst 228 -24.98 -3.92 3.89e+01 1fmb 104 -23.03 -3.90 4.00e+01