% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (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-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. % --------------------------------------------------------------------- % str2foo.1.YCR102W-A.t2k-100-30-str2 Host: farm18 Mon Nov 29 12:06:58 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YCR1/YCR102W-A % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.str2s % % 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 YCR102W-A.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YCR102W-A.t2k.str2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10944 sequences, 2597075 residues, 66 nodes, 73.17 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 (=10700) sequences: % N / (1 + exp(-(lambda(=3.0212) * Reverse)^tau(=0.6635))) % 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 1ffkU 91 -15.67 -7.60 3.61e+00 1te2A 226 -15.33 -7.19 4.80e+00 1dszB 85 -14.55 -7.13 5.01e+00 1rxr 83 -14.62 -7.12 5.05e+00 1x92A 199 -14.76 -6.74 6.65e+00 1jj2W 91 -15.30 -6.62 7.24e+00 1s72X 92 -15.29 -6.62 7.27e+00 1h75A 81 -13.44 -6.54 7.70e+00 1mp8A 281 -14.78 -6.53 7.75e+00 1hra 81 -14.25 -6.51 7.84e+00 1gyxA 76 -14.93 -6.50 7.91e+00 1pprM 312 -16.79 -6.36 8.75e+00 2nllA 66 -13.88 -6.31 9.11e+00 1dszA 86 -14.05 -6.30 9.17e+00 1mn8A 100 -14.90 -6.19 9.96e+00 1mc2A 122 -14.31 -6.08 1.08e+01 1adt 356 -15.07 -6.03 1.12e+01 1jw3A 140 -14.08 -5.94 1.20e+01 1mp1A 111 -15.04 -5.92 1.22e+01 1anv 356 -14.68 -5.78 1.36e+01 2nllB 103 -14.09 -5.69 1.46e+01 1ur3M 319 -13.39 -5.57 1.59e+01 1kyoG 126 -15.26 -5.57 1.59e+01 1dpe 507 -13.42 -5.54 1.64e+01 1ha8A 51 -14.61 -5.47 1.72e+01 1kb9G 125 -15.28 -5.45 1.75e+01 1ezvF 125 -15.28 -5.45 1.75e+01 1rw2A 152 -13.52 -5.41 1.80e+01 1h65A 270 -13.86 -5.38 1.84e+01 1ki1B 352 -14.12 -5.37 1.86e+01 1ga0A 364 -12.69 -5.21 2.11e+01 1mk0A 97 -13.25 -5.16 2.19e+01 1gceA 364 -12.68 -5.16 2.20e+01 1dppA 507 -13.15 -5.15 2.22e+01 1onhA 364 -12.69 -5.13 2.25e+01 1uf3A 228 -12.20 -5.10 2.30e+01 1og6A 298 -13.03 -5.10 2.31e+01 1fgkA 310 -13.47 -5.07 2.37e+01 1mszA 86 -13.08 -5.02 2.47e+01 1gs5A 258 -12.98 -4.96 2.59e+01 1sly 618 -14.61 -4.86 2.79e+01 2arcA 164 -13.04 -4.86 2.80e+01 1jhb 106 -12.18 -4.82 2.88e+01 2arcB 164 -13.05 -4.80 2.94e+01 2bltA 361 -12.33 -4.70 3.17e+01 1iqrA 420 -14.26 -4.70 3.18e+01 1q2zA 120 -13.13 -4.70 3.18e+01 1rvgA 305 -12.74 -4.69 3.20e+01 1ig6A 107 -14.26 -4.69 3.21e+01 1pszA 303 -13.58 -4.67 3.27e+01 1qf5A 431 -12.93 -4.56 3.57e+01 1eh2 106 -14.56 -4.55 3.61e+01 1aw0 72 -10.96 -4.49 3.80e+01 1h3oA 75 -12.28 -4.43 3.97e+01 2aacA 177 -12.97 -4.43 3.97e+01