% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 07/18/05_14:54:13 % (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-T2K, 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, et al., What is the value added by human intervention in protein % structure prediction, Proteins: Stucture, Function, Genetics 45(S5):86--91, 2001. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YBR221W-A.t2k-100-30-dssp-ehl2 Host: farm02.cse.ucsc.edu Mon Feb 13 11:51:58 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YBR2/YBR221W-A % --------------------------------------------------------------------- % 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 +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YBR221W-A.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YBR221W-A.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13614 sequences, 3208521 residues, 35 nodes, 56.86 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 (10000.00) % E-value on N (=11000) sequences: % N / (1 + exp(-(lambda(=5.6031) * Reverse)^tau(=0.6362))) % Calculated when Simple < simple_threshold (10000.00) % 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 1qwtA 255 -13.98 -6.12 8.45e-01 1h4aX 173 -12.82 -6.08 8.73e-01 1kolA 398 -13.58 -5.97 9.75e-01 1r8oA 96 -13.65 -5.53 1.52e+00 1r61A 207 -14.11 -5.47 1.62e+00 1m15A 357 -11.62 -5.02 2.58e+00 1bg0 356 -11.63 -5.01 2.61e+00 1grj 158 -11.61 -5.01 2.62e+00 1pse 69 -11.67 -4.75 3.46e+00 1oqqA 106 -10.68 -4.51 4.49e+00 1put 106 -10.51 -4.25 5.98e+00 3mddA 385 -10.18 -4.01 7.91e+00 3mdeA 385 -10.18 -3.97 8.25e+00 1n1tA 641 -11.91 -3.84 9.53e+00 1w8oA 601 -12.49 -3.67 1.16e+01 1wcqA 601 -12.50 -3.67 1.17e+01 1euu 605 -12.49 -3.67 1.18e+01 1q48A 134 -11.08 -3.65 1.19e+01 1eut 605 -12.50 -3.59 1.28e+01 1r6rA 100 -9.57 -3.55 1.35e+01 1rtu 114 -10.16 -3.52 1.40e+01 1egdA 396 -10.13 -3.50 1.43e+01 1abwA 283 -8.81 -3.50 1.43e+01 1elpA 173 -10.14 -3.43 1.56e+01 1d6zA 727 -10.70 -3.41 1.59e+01 1spuB 727 -10.70 -3.38 1.66e+01 1xlqA 106 -9.46 -3.38 1.66e+01 1oacA 727 -10.71 -3.36 1.69e+01 1zlqA 502 -10.10 -3.30 1.82e+01 1a4yB 123 -10.28 -3.29 1.85e+01 1i17A 107 -9.65 -3.28 1.86e+01 1uiuA 502 -10.10 -3.28 1.88e+01 1j7yA 141 -8.45 -3.27 1.90e+01 1pwt 61 -9.92 -3.27 1.90e+01 1xizA 159 -9.96 -3.26 1.91e+01 1tud 62 -9.90 -3.26 1.91e+01 1g2bA 62 -9.89 -3.26 1.92e+01 1shg 62 -9.90 -3.25 1.95e+01 1zsqA 528 -10.04 -3.24 1.97e+01 1zlhB 75 -9.24 -3.23 2.00e+01 1amm 174 -9.79 -3.17 2.16e+01 4gcr 174 -9.79 -3.17 2.16e+01 1bshA 138 -10.08 -3.15 2.21e+01 2rspA 124 -10.77 -3.14 2.23e+01 1irdA 141 -8.33 -3.13 2.27e+01 2rspB 124 -10.79 -3.12 2.29e+01 1babA 143 -8.32 -3.10 2.35e+01 1txb 73 -10.29 -3.05 2.50e+01 1ugpB 226 -11.59 -2.98 2.72e+01 1ireB 228 -11.59 -2.98 2.72e+01 1ocnA 362 -10.05 -2.97 2.76e+01 2bvwA 362 -10.05 -2.97 2.76e+01 1bvwA 360 -10.06 -2.97 2.77e+01 1fc6A 388 -10.10 -2.97 2.78e+01 1jceA 344 -9.65 -2.96 2.82e+01 1oc7A 364 -10.05 -2.95 2.85e+01 1jpyA 137 -9.82 -2.92 2.93e+01 1o4wA 147 -9.12 -2.91 2.99e+01 1k5nA 276 -9.86 -2.90 3.01e+01 1mvpA 124 -10.12 -2.90 3.01e+01 1lw3A 657 -9.82 -2.90 3.02e+01 1jcfA 344 -9.61 -2.89 3.06e+01 1fs0E 138 -9.42 -2.88 3.11e+01 1uwvA 433 -9.61 -2.86 3.17e+01 2ai4A 119 -9.52 -2.85 3.24e+01 1pm6A 72 -10.39 -2.84 3.28e+01 1v84A 253 -9.82 -2.84 3.29e+01 1jpyB 137 -9.83 -2.82 3.34e+01 1kzyC 259 -9.57 -2.82 3.36e+01 1iwhA 141 -8.08 -2.81 3.39e+01 1k59A 123 -9.66 -2.81 3.39e+01 1aqt 138 -9.31 -2.80 3.43e+01 1agdA 276 -9.73 -2.79 3.51e+01 1sqzA 121 -9.16 -2.78 3.52e+01 1tk4A 121 -9.16 -2.78 3.52e+01 1zwpA 121 -9.16 -2.78 3.52e+01 1ms9A 648 -10.77 -2.78 3.53e+01 1hbyA 123 -9.67 -2.78 3.54e+01 1tj9A 121 -9.16 -2.78 3.54e+01 1fv0A 121 -9.16 -2.78 3.55e+01 1kpmA 121 -9.16 -2.78 3.55e+01 3dni 260 -9.42 -2.77 3.59e+01 2dnjA 260 -9.41 -2.75 3.69e+01 2bwkA 121 -9.32 -2.69 3.98e+01