% 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. % --------------------------------------------------------------------- % dsspfoo.1.YGR025W.t2k-100-30-dssp-ebghstl Host: cc47 Fri Nov 8 17:40:43 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-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7310 sequences, 1706072 residues, 101 nodes, 67.75 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(=2.2268) * Reverse)^tau(=0.7471))) % 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 1jroB 777 -30.73 -8.38 9.97e-01 1irk 306 -26.98 -7.23 2.52e+00 1j6nA 303 -26.33 -7.20 2.59e+00 1lba 146 -25.76 -7.10 2.80e+00 1ddt 535 -28.13 -6.78 3.65e+00 1dfnA 30 -21.92 -6.60 4.25e+00 1ir3A 306 -26.19 -6.48 4.70e+00 1mak 113 -25.11 -6.43 4.91e+00 1icfA 175 -25.46 -6.34 5.32e+00 1jpaA 312 -26.77 -6.24 5.76e+00 1g0sA 209 -26.49 -6.21 5.92e+00 1hxmA 229 -27.60 -6.20 5.96e+00 1i2hA 168 -24.98 -5.84 8.14e+00 1qppA 218 -27.10 -5.82 8.33e+00 1ddvA 111 -24.31 -5.75 8.83e+00 1apyB 141 -23.66 -5.71 9.10e+00 1ddwA 120 -24.28 -5.71 9.14e+00 1eaiC 61 -24.42 -5.64 9.71e+00 1f0lA 535 -26.90 -5.59 1.02e+01 1qr6A 584 -27.16 -5.57 1.04e+01 1slvA 142 -26.25 -5.41 1.19e+01 1ihgA 370 -27.63 -5.35 1.25e+01 1ib8A 164 -24.42 -5.14 1.51e+01 1kyqA 274 -24.59 -5.04 1.65e+01 1sluA 142 -26.06 -5.03 1.67e+01 2plc 274 -25.11 -5.02 1.68e+01 1je5A 206 -25.91 -5.01 1.69e+01 1a1z 91 -20.49 -5.00 1.72e+01 1jm7B 117 -23.96 -4.98 1.75e+01 1dqsA 393 -25.38 -4.96 1.77e+01 1pdgC 109 -26.78 -4.95 1.80e+01 1cs8A 316 -25.97 -4.94 1.81e+01 1iqaA 160 -24.32 -4.94 1.81e+01 1nglA 179 -25.84 -4.83 1.99e+01 1a1w 91 -20.24 -4.76 2.12e+01 1pdgA 109 -26.62 -4.73 2.19e+01 1am2 199 -24.33 -4.55 2.58e+01 1rhd 293 -23.91 -4.43 2.89e+01 1iwgA 1053 -26.93 -4.43 2.90e+01 1qmeA 702 -26.62 -4.37 3.05e+01 1rhs 296 -23.84 -4.34 3.15e+01 1ggvA 232 -23.45 -4.32 3.20e+01 1l0oA 150 -22.47 -4.29 3.29e+01 1din 236 -23.47 -4.27 3.37e+01 1a3lL 217 -24.70 -4.22 3.52e+01 1kkhA 317 -24.20 -4.21 3.54e+01