% 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. % --------------------------------------------------------------------- % w0.5foo.1.YGR022C.t2k-w0.5.mod Host: cc51 Fri Nov 8 17:14:07 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR022C % --------------------------------------------------------------------- % Inserted Files: YGR022C.t2k-w0.5.mod % Database Files: /projects/compbio/experiments/protein-predict/SAM_T02/data/pdbaa % % 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)) % Single Track Model: YGR022C.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13975 sequences, 3107935 residues, 110 nodes, 108.29 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(=2.8671) * Reverse)^tau(=0.7726))) % 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 1in6A 334 -27.28 -7.03 2.76e-01 1c0pA 363 -26.86 -6.71 3.98e-01 1in7A 334 -26.40 -6.17 7.33e-01 1in4A 334 -26.40 -6.16 7.46e-01 1in5A 334 -26.40 -6.15 7.55e-01 1j7kA 334 -26.40 -6.14 7.63e-01 1in8A 334 -26.40 -6.11 7.86e-01 1c7nA 399 -26.04 -5.80 1.13e+00 1grj 158 -23.89 -5.13 2.50e+00 1bdyA 123 -22.51 -5.04 2.79e+00 1d3bB 91 -21.72 -4.44 5.78e+00 1h4wA 224 -23.26 -4.39 6.18e+00 1g291 372 -24.72 -4.30 6.92e+00 1f4tA 368 -24.47 -4.19 7.95e+00 1io7A 368 -24.47 -4.19 7.95e+00 1io8A 368 -24.47 -4.18 8.02e+00 1igl 67 -21.09 -4.18 8.06e+00 1j5wA 298 -24.72 -4.00 1.01e+01 1bia 321 -24.20 -3.96 1.06e+01 1bib 321 -24.20 -3.96 1.06e+01 1evsA 187 -22.64 -3.95 1.07e+01 1qjoA 80 -20.79 -3.90 1.15e+01 1jgtA 513 -25.11 -3.79 1.32e+01 1gwjA 377 -24.16 -3.77 1.35e+01 1h61A 364 -23.98 -3.74 1.40e+01 1kk1A 410 -24.66 -3.73 1.42e+01 1bt0A 76 -20.52 -3.73 1.43e+01 1faaA 124 -21.52 -3.70 1.48e+01 1b2pA 119 -21.37 -3.64 1.61e+01 3sicI 107 -21.04 -3.58 1.73e+01 1zfo 31 -18.18 -3.56 1.78e+01 1dpo 223 -23.32 -3.55 1.80e+01 2sicI 107 -20.99 -3.53 1.84e+01 1a0fA 201 -22.38 -3.51 1.91e+01 3ssi 113 -21.05 -3.51 1.91e+01 1nddA 76 -20.56 -3.50 1.91e+01 1nddD 76 -20.56 -3.50 1.91e+01 1qe3A 489 -24.26 -3.49 1.94e+01 1c7iA 489 -24.19 -3.49 1.95e+01 1i7mA 267 -23.02 -3.46 2.01e+01 1qspA 165 -21.67 -3.42 2.13e+01 1l0wA 580 -25.09 -3.42 2.13e+01 1c03A 168 -21.69 -3.42 2.13e+01 1cyw 205 -21.78 -3.36 2.30e+01 1iq4A 179 -22.21 -3.30 2.48e+01 1hmr 132 -21.55 -3.29 2.52e+01 1hms 132 -21.55 -3.29 2.52e+01 1hmt 132 -21.55 -3.29 2.52e+01 1k9oE 223 -23.01 -3.26 2.63e+01 1jenA 267 -22.64 -3.25 2.68e+01 1ayfB 105 -20.97 -3.23 2.74e+01 1ayfA 105 -20.97 -3.23 2.74e+01 1i7cA 267 -22.64 -3.23 2.76e+01 3tgjE 233 -23.06 -3.22 2.76e+01 1tfxC 58 -19.96 -3.22 2.77e+01 1br2A 791 -25.36 -3.21 2.80e+01 2tnfA 156 -21.77 -3.21 2.81e+01 1hznA 31 -17.18 -3.21 2.82e+01 1tubB 427 -23.89 -3.21 2.82e+01 1c02A 166 -21.41 -3.19 2.89e+01 1adz 71 -20.35 -3.19 2.91e+01 1ju3A 583 -24.74 -3.18 2.94e+01 1fx0B 498 -24.59 -3.18 2.95e+01 1l6uA 128 -21.27 -3.17 2.95e+01 1e6eB 128 -21.27 -3.17 2.97e+01 1l6vA 128 -21.26 -3.17 2.98e+01 1slwB 223 -22.75 -3.16 3.00e+01 1fts 295 -23.01 -3.15 3.06e+01 1cjeB 127 -21.22 -3.14 3.08e+01 1br1A 820 -25.40 -3.11 3.23e+01 1ivhA 394 -23.73 -3.10 3.25e+01 1slxB 223 -22.75 -3.10 3.27e+01 1isnA 323 -22.92 -3.07 3.40e+01 3tgkE 231 -22.91 -3.06 3.43e+01 1h6vE 499 -25.81 -3.06 3.44e+01 1ia0B 445 -23.93 -3.05 3.48e+01 1lwuA 119 -20.74 -3.04 3.52e+01 1mpgA 282 -22.45 -3.03 3.58e+01 1bwvS 138 -20.79 -3.02 3.62e+01 1h4rB 314 -22.96 -2.99 3.77e+01 1h4rA 314 -22.96 -2.99 3.78e+01 1anc 223 -22.76 -2.98 3.85e+01 1ezsC 223 -22.73 -2.97 3.88e+01 2trm 223 -22.73 -2.97 3.88e+01 1and 223 -22.73 -2.96 3.92e+01 1ane 223 -22.74 -2.96 3.95e+01 1f5rA 231 -22.77 -2.96 3.95e+01 1qtfA 246 -22.55 -2.95 3.98e+01