% 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. % --------------------------------------------------------------------- % CB_burial_14_7foo.1.YGR213C.t2k-100-30-CB_burial_14_7 Host: farm01 Wed Dec 1 19:04:56 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR213C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/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 YGR213C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR213C.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10944 sequences, 2597075 residues, 318 nodes, 340.58 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(=2.1949) * Reverse)^tau(=0.7673))) % 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 6prcH 258 -22.80 -8.07 1.22e+00 1otjA 283 -19.75 -7.83 1.51e+00 1gy9A 283 -20.40 -7.82 1.52e+00 1dxrH 258 -22.58 -7.71 1.68e+00 1gqwA 283 -20.05 -7.37 2.26e+00 1b3rA 431 -17.88 -7.04 3.01e+00 1mixA 206 -18.05 -6.74 3.96e+00 1tlqA 189 -17.31 -6.70 4.08e+00 1d4fA 431 -17.88 -6.70 4.09e+00 1a7aA 432 -17.80 -6.70 4.11e+00 1gj7B 253 -16.10 -6.58 4.59e+00 1vjgA 218 -16.24 -6.50 4.90e+00 1uynX 308 -15.47 -6.33 5.71e+00 1lzlA 323 -17.08 -6.30 5.88e+00 1s72M 194 -20.94 -6.29 5.93e+00 1li4A 432 -17.24 -6.19 6.55e+00 1c5yB 253 -15.50 -5.93 8.30e+00 1eqnA 321 -17.77 -5.91 8.42e+00 1a99A 344 -15.59 -5.86 8.81e+00 1pjhA 280 -16.52 -5.71 1.02e+01 1gdgA 293 -15.44 -5.66 1.07e+01 1dhy 292 -15.06 -5.65 1.07e+01 1p0hA 318 -15.70 -5.61 1.11e+01 1gk8I 140 -17.81 -5.48 1.26e+01 1g55A 343 -16.30 -5.46 1.28e+01 1b6g 310 -15.13 -5.36 1.42e+01 1suwA 249 -15.60 -5.33 1.46e+01 1dd9A 338 -16.70 -5.27 1.54e+01 1kgyA 181 -15.83 -5.27 1.54e+01 1nnsA 326 -15.18 -5.19 1.66e+01 1js1X 324 -16.56 -5.18 1.68e+01 1jjiA 311 -16.03 -5.14 1.74e+01 1kw3B 292 -14.86 -5.14 1.74e+01 1shwB 181 -16.02 -5.05 1.90e+01 1vjhA 122 -17.29 -5.00 1.99e+01 1ir21 140 -16.85 -4.98 2.04e+01 3pga1 337 -14.56 -4.97 2.05e+01 1t0yA 122 -16.74 -4.96 2.07e+01 1li5A 461 -15.51 -4.93 2.13e+01 1ddwA 120 -15.45 -4.92 2.14e+01 1ev0A 58 -18.78 -4.85 2.30e+01 1ede 310 -14.65 -4.80 2.42e+01 1b71A 191 -14.53 -4.71 2.65e+01 1jnrB 150 -20.80 -4.64 2.83e+01 1k9dA 679 -14.62 -4.59 2.97e+01 1w9pA 433 -15.34 -4.53 3.15e+01 1l6rA 227 -15.28 -4.52 3.18e+01 1ryt 190 -14.75 -4.52 3.19e+01 1dvbA 191 -14.54 -4.51 3.22e+01 1j1bA 420 -16.98 -4.51 3.22e+01 1jmeA 455 -15.12 -4.49 3.28e+01 1b8qA 127 -14.92 -4.46 3.36e+01 1ddeA 338 -16.00 -4.46 3.37e+01 1d7qA 143 -23.77 -4.44 3.43e+01 1pwhA 327 -14.58 -4.43 3.46e+01 1hn6A 110 -22.40 -4.43 3.46e+01 1ddvA 111 -15.11 -4.41 3.54e+01 1mzjA 339 -16.09 -4.41 3.55e+01 1g8jA 825 -15.60 -4.40 3.58e+01 1eysH 259 -18.41 -4.39 3.61e+01 1lkoA 191 -14.48 -4.37 3.67e+01 1is2A 661 -16.65 -4.37 3.69e+01 1j6nA 303 -14.35 -4.36 3.71e+01 1o58A 303 -14.35 -4.35 3.74e+01 1j0aA 325 -14.81 -4.35 3.78e+01 1n8yC 608 -15.88 -4.34 3.78e+01 1dbqA 289 -15.28 -4.29 3.99e+01