% 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. % --------------------------------------------------------------------- % CB_burial_14_7foo.1.YGR035W-A.t2k-100-40-40-str2+CB_burial_14_7 Host: farm09.cse.ucsc.edu Sun Feb 12 22:17:55 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR035W-A % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.str2s,/projects/compbio/experiments/models.97/indexes/t2k.CB-burial-14-7s % % 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 YGR035W-A.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.400 File YGR035W-A.t2k.str2.mod % Track 2 FIMs added (the generic node (5)) % Track 2 Coeff 0.400 File YGR035W-A.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13614 sequences, 3208521 residues, 74 nodes, 126.09 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(=1.3665) * Reverse)^tau(=0.8643))) % 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 1tc5A 194 -21.35 -11.83 1.69e-01 1aayA 90 -20.49 -10.86 3.74e-01 1f75A 249 -20.31 -10.82 3.86e-01 1zaaC 87 -20.23 -10.57 4.73e-01 1a1iA 90 -19.65 -10.04 7.35e-01 1rlyA 60 -21.43 -9.85 8.55e-01 1dl6A 58 -21.13 -9.85 8.55e-01 4rxn 54 -23.56 -9.75 9.29e-01 1jnrB 150 -22.01 -9.34 1.31e+00 1hn6A 110 -21.81 -9.29 1.37e+00 1g2fC 90 -19.04 -9.16 1.52e+00 1g8oA 310 -18.46 -9.06 1.66e+00 1plfA 72 -18.67 -8.78 2.09e+00 2f4lA 297 -19.51 -8.69 2.26e+00 1udh 244 -17.87 -8.64 2.36e+00 1yc61 154 -19.71 -8.55 2.54e+00 1avyA 74 -21.17 -8.45 2.77e+00 1wf9A 107 -19.15 -8.24 3.31e+00 1uehA 253 -16.87 -8.10 3.72e+00 1humA 69 -18.08 -8.05 3.89e+00 1jp3A 253 -16.65 -7.87 4.53e+00 1lldA 319 -18.22 -7.87 4.54e+00 1z3eA 132 -17.73 -7.80 4.82e+00 1ehkB 168 -21.77 -7.76 5.00e+00 1iro 54 -21.86 -7.74 5.10e+00 1xaoA 121 -17.36 -7.71 5.22e+00 2a4hA 126 -19.10 -7.54 6.01e+00 1avyC 74 -20.13 -7.54 6.02e+00 1vcbA 118 -18.06 -7.54 6.05e+00 2anwA 241 -16.80 -7.53 6.11e+00 2anyA 241 -16.41 -7.50 6.25e+00 1qwtA 255 -17.24 -7.47 6.38e+00 1ni4A 365 -17.32 -7.46 6.45e+00 1v5vA 401 -16.11 -7.34 7.13e+00 1b5qA 472 -16.79 -7.31 7.36e+00 1b37A 472 -16.79 -7.29 7.51e+00 1t3nA 388 -16.48 -7.22 7.93e+00 1a31A 538 -17.06 -7.22 7.93e+00 1wthD 391 -18.04 -7.18 8.22e+00 8acn 754 -16.70 -7.17 8.33e+00 1f7tA 122 -16.94 -7.15 8.44e+00 1mnnA 340 -16.99 -7.12 8.65e+00 1k4tA 592 -17.43 -7.07 9.05e+00 1pv9A 348 -16.81 -7.06 9.12e+00 6acn 754 -16.61 -7.02 9.48e+00 2bsdA 264 -17.19 -7.02 9.48e+00 1amj 754 -16.53 -7.00 9.61e+00 7acn 754 -16.46 -6.96 9.93e+00 1qa7B 217 -16.91 -6.90 1.05e+01 1v87A 114 -16.66 -6.90 1.05e+01 1r5tA 142 -15.50 -6.84 1.10e+01 2fftA 84 -21.72 -6.78 1.17e+01 1prcC 336 -16.46 -6.76 1.18e+01 1a36A 592 -16.62 -6.73 1.22e+01 1f7lA 121 -15.92 -6.65 1.31e+01 1cjsA 219 -15.73 -6.64 1.31e+01 1frrA 95 -15.46 -6.60 1.37e+01 1c96A 753 -16.11 -6.58 1.39e+01 1rwjA 82 -17.08 -6.49 1.50e+01 1xgyL 216 -16.81 -6.42 1.59e+01 1bxeA 113 -14.99 -6.42 1.60e+01 1vr7A 142 -14.09 -6.40 1.62e+01 1qlpA 394 -15.56 -6.40 1.62e+01 1tzpA 255 -15.28 -6.38 1.65e+01 1vkbA 161 -15.44 -6.37 1.66e+01 1b37B 472 -15.63 -6.27 1.83e+01 1i2aA 219 -15.26 -6.19 1.95e+01 1xxsA 122 -17.35 -6.17 1.98e+01 1na6A 404 -16.04 -6.17 1.98e+01 1b0jA 754 -15.40 -6.14 2.04e+01 1taq 832 -16.70 -6.11 2.10e+01 1havA 217 -16.03 -6.08 2.15e+01 2occG 84 -17.84 -6.08 2.16e+01 1dwkA 156 -18.28 -6.06 2.19e+01 1dw9A 156 -18.35 -6.06 2.19e+01 2aw4Z 70 -18.20 -6.05 2.21e+01 1niyA 36 -15.28 -6.04 2.23e+01 2b1xA 470 -16.01 -6.03 2.26e+01 2sniI 83 -15.65 -6.02 2.26e+01 1i7nA 309 -15.08 -5.94 2.44e+01 1lm8B 118 -17.56 -5.93 2.46e+01 1sfe 180 -13.73 -5.91 2.50e+01 1v54G 85 -17.64 -5.88 2.56e+01 1brfA 53 -18.80 -5.85 2.64e+01 1vqvA 306 -14.70 -5.83 2.68e+01 1a0hA 159 -20.50 -5.80 2.75e+01 1lylA 504 -16.34 -5.80 2.75e+01 1pdkB 157 -15.37 -5.80 2.75e+01 1cqxA 403 -15.64 -5.80 2.76e+01 1jlxA 304 -15.78 -5.80 2.77e+01 1uoyA 64 -15.46 -5.79 2.78e+01 1udg 244 -14.52 -5.78 2.82e+01 1vajA 214 -15.37 -5.77 2.83e+01 1zbdB 134 -16.98 -5.75 2.90e+01 2cszA 76 -21.39 -5.74 2.92e+01 1ml0D 76 -15.44 -5.73 2.95e+01 1cm9A 74 -16.82 -5.67 3.09e+01 2aw4R 103 -15.50 -5.66 3.13e+01 1nyoA 163 -13.26 -5.65 3.14e+01 1auyA 189 -15.10 -5.65 3.15e+01 2occF 98 -15.82 -5.63 3.22e+01 1y4lA 121 -16.42 -5.58 3.35e+01 1pvuA 154 -15.50 -5.58 3.36e+01 1v54F 98 -16.34 -5.57 3.37e+01 1nepA 130 -15.99 -5.57 3.37e+01 1e1oA 504 -15.81 -5.55 3.46e+01 1fc1A 224 -15.74 -5.52 3.54e+01 1i81A 83 -15.71 -5.52 3.54e+01 1jlyA 304 -15.58 -5.49 3.62e+01 1bq9A 54 -18.53 -5.49 3.66e+01 1ff4A 65 -15.12 -5.47 3.72e+01 1h8eI 50 -15.00 -5.46 3.72e+01 1mcpL 220 -14.81 -5.46 3.76e+01 1s48A 609 -14.78 -5.44 3.80e+01 1m3sA 186 -13.96 -5.39 3.97e+01 1mxmA 254 -18.61 -5.39 3.97e+01