% 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. % --------------------------------------------------------------------- % strfoo.1.YGR035C.t2k-100-30-str Host: cc41 Fri Nov 8 18:53:36 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR035C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.strs % % 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 YGR035C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR035C.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 117 nodes, 78.62 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(=2.0765) * Reverse)^tau(=0.7785))) % 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 1a3gA 308 -29.79 -9.54 2.65e-01 1l2rA 458 -29.98 -8.27 7.76e-01 1l2qA 458 -29.98 -8.27 7.77e-01 1i1kA 309 -27.60 -7.55 1.45e+00 1ggvA 232 -26.99 -7.22 1.94e+00 1kqfC 217 -27.80 -6.75 2.97e+00 1lba 146 -25.26 -6.61 3.37e+00 1fj2A 232 -25.88 -6.52 3.64e+00 1noyA 388 -28.65 -6.37 4.20e+00 1oyc 400 -27.30 -6.22 4.78e+00 1qatB 622 -29.07 -6.12 5.25e+00 1din 236 -26.59 -6.11 5.32e+00 1gtzA 156 -24.23 -6.07 5.49e+00 1oya 400 -26.98 -5.97 6.06e+00 1d0iA 156 -24.29 -5.95 6.16e+00 1qasA 622 -28.72 -5.88 6.58e+00 3pmgA 561 -28.63 -5.81 6.98e+00 1c4zA 358 -26.79 -5.81 7.02e+00 1djxB 624 -28.49 -5.71 7.67e+00 1djxA 624 -28.46 -5.71 7.69e+00 1oyb 400 -26.71 -5.58 8.70e+00 1hlrA 907 -28.40 -5.36 1.07e+01 7atjA 308 -27.32 -5.28 1.16e+01 2atjA 308 -27.30 -5.26 1.18e+01 1jy5A 212 -24.97 -5.19 1.25e+01 1jmoA 480 -28.05 -5.13 1.33e+01 1xnb 185 -23.24 -5.12 1.34e+01 1qc5A 192 -23.88 -5.09 1.38e+01 1imjA 210 -24.99 -5.08 1.39e+01 1jqgA 433 -25.82 -5.07 1.41e+01 1vtp 26 -18.90 -5.06 1.43e+01 1bmlC 362 -27.10 -4.99 1.53e+01 1jkgA 140 -22.76 -4.94 1.60e+01 1e9kA 38 -19.70 -4.84 1.75e+01 1cb0A 283 -26.34 -4.81 1.80e+01 1epuA 591 -26.58 -4.76 1.89e+01 1ako 268 -24.71 -4.75 1.93e+01 1c4xA 285 -24.65 -4.74 1.94e+01 1k8kD 300 -30.32 -4.72 1.98e+01 1ee4A 423 -26.17 -4.71 1.99e+01 1wad 112 -22.34 -4.69 2.03e+01 1gc1G 321 -25.53 -4.64 2.14e+01 1qmhA 347 -25.09 -4.63 2.16e+01 1jn5A 140 -22.44 -4.60 2.21e+01 1hxpA 348 -25.38 -4.55 2.33e+01 1hllA 32 -19.47 -4.54 2.37e+01 1bpv 112 -21.95 -4.53 2.37e+01 1g73A 162 -23.00 -4.51 2.43e+01 1k4wA 252 -25.16 -4.48 2.50e+01 1qe3A 489 -26.35 -4.47 2.51e+01 1jjiA 311 -25.05 -4.42 2.65e+01 1dhpA 292 -24.56 -4.40 2.70e+01 1i3jA 116 -22.66 -4.37 2.79e+01 1atiB 505 -26.22 -4.34 2.86e+01 1atiA 505 -26.22 -4.34 2.86e+01 1ospO 257 -23.53 -4.32 2.93e+01 1vfbA 107 -21.26 -4.31 2.97e+01 1a2yA 107 -21.26 -4.30 2.99e+01 1j6rA 214 -25.91 -4.28 3.05e+01 1l1oC 181 -22.94 -4.27 3.07e+01 1gupA 348 -25.11 -4.25 3.13e+01 1g7jA 107 -21.26 -4.23 3.19e+01 1guqA 348 -25.11 -4.23 3.21e+01 1di0A 158 -22.87 -4.20 3.29e+01 1inlA 296 -24.41 -4.20 3.31e+01 1qhtA 775 -27.83 -4.16 3.43e+01 1f45B 197 -24.26 -4.15 3.45e+01 1k4cC 124 -22.91 -4.15 3.46e+01 1bn7A 294 -24.20 -4.12 3.58e+01 1k6zA 141 -24.39 -4.10 3.66e+01 1bn6A 294 -24.17 -4.06 3.81e+01 1jyaA 130 -23.98 -4.05 3.82e+01 1cjcA 460 -25.53 -4.05 3.84e+01 1jq3A 296 -24.39 -4.04 3.85e+01 1lxtA 561 -27.69 -4.03 3.90e+01 1eziA 228 -24.09 -4.02 3.96e+01 1cqwA 295 -24.18 -4.01 3.98e+01