% 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.YGR016W.t2k-100-30-str Host: cc41 Fri Nov 8 16:57:42 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR016W % --------------------------------------------------------------------- % 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 YGR016W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR016W.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7310 sequences, 1706072 residues, 191 nodes, 128.22 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(=1.8377) * Reverse)^tau(=0.7567))) % 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 1g5hA 454 -35.22 -11.87 2.45e-01 1f00I 282 -28.46 -8.33 2.75e+00 1ap6A 198 -29.01 -8.08 3.30e+00 1abmA 198 -29.19 -8.01 3.47e+00 1yprA 125 -28.49 -8.01 3.47e+00 1g99A 408 -30.55 -7.75 4.18e+00 1dofA 403 -30.88 -7.48 5.11e+00 1yasA 257 -27.84 -7.23 6.13e+00 1go5A 69 -24.94 -6.94 7.61e+00 1hzpA 335 -27.80 -6.89 7.90e+00 1howA 373 -29.93 -6.78 8.58e+00 1qj4A 257 -27.10 -6.56 1.02e+01 1qklA 127 -25.90 -6.47 1.08e+01 1gg3A 279 -28.30 -6.44 1.11e+01 2btfA 375 -28.32 -6.41 1.14e+01 1hv2A 99 -26.54 -6.34 1.20e+01 1dgaA 375 -28.45 -6.19 1.35e+01 1d4xA 375 -28.52 -6.15 1.38e+01 1lmb3 92 -24.49 -6.08 1.46e+01 1h6zA 913 -30.16 -6.08 1.46e+01 1a0k 131 -27.20 -5.95 1.62e+01 1k8kA 418 -28.54 -5.94 1.63e+01 3nul 130 -26.99 -5.84 1.77e+01 1reqB 637 -28.50 -5.76 1.88e+01 1lliA 92 -24.06 -5.73 1.92e+01 1gv3A 248 -27.87 -5.69 1.98e+01 1yagA 375 -28.31 -5.69 1.99e+01 1pyaB 228 -27.60 -5.63 2.08e+01 1reqD 637 -28.30 -5.56 2.20e+01 1b43A 340 -27.42 -5.49 2.33e+01 1hnoA 280 -26.75 -5.10 3.17e+01 1a81A 254 -25.99 -5.10 3.17e+01 1knqA 175 -26.25 -5.08 3.21e+01 1et0A 269 -26.13 -5.06 3.26e+01 1cjaA 342 -28.15 -5.05 3.29e+01 1pbwA 216 -26.21 -5.04 3.32e+01 1bmfA 510 -27.43 -4.99 3.47e+01 1j6zA 376 -26.83 -4.92 3.66e+01 1kafA 108 -25.26 -4.90 3.72e+01 1i7gA 287 -27.77 -4.86 3.84e+01 1bebA 162 -25.38 -4.82 3.97e+01