% 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. % --------------------------------------------------------------------- % stridefoo.1.YGR024C.t2k-100-30-stride-ebghtl Host: cc69 Fri Nov 8 17:55:38 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR024C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.2ds % % 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 YGR024C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR024C.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7310 sequences, 1706072 residues, 238 nodes, 162.15 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(=1.2489) * Reverse)^tau(=0.8624))) % 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 1qgwC 177 -32.49 -11.33 3.95e-01 1hbp 183 -30.85 -9.96 1.11e+00 1hbq 183 -30.85 -9.96 1.11e+00 1aqb 183 -30.68 -9.92 1.15e+00 1ezm 301 -33.66 -9.84 1.21e+00 1jyoA 130 -29.84 -9.37 1.74e+00 1hm6A 346 -31.85 -9.16 2.05e+00 1f2tB 148 -32.77 -8.80 2.70e+00 1j77A 209 -33.06 -8.78 2.74e+00 1jf0A 195 -30.08 -8.62 3.10e+00 1hv8A 367 -32.95 -8.49 3.45e+00 1k3eA 156 -30.50 -8.25 4.14e+00 1a8y 367 -31.89 -8.25 4.14e+00 9apiA 347 -30.26 -8.15 4.49e+00 1qkmA 255 -32.20 -8.13 4.56e+00 1cuk 203 -30.09 -7.98 5.12e+00 1ayyA 151 -27.66 -7.93 5.32e+00 1go4A 205 -34.14 -7.88 5.54e+00 1g24A 211 -28.44 -7.66 6.57e+00 1c1dA 355 -30.83 -7.66 6.59e+00 1rbp 182 -28.23 -7.57 7.05e+00 1a0p 290 -30.66 -7.55 7.19e+00 1hjp 203 -30.50 -7.54 7.25e+00 1qlpA 394 -29.69 -7.54 7.25e+00 1bw9A 356 -30.69 -7.52 7.34e+00 1kq4A 232 -31.53 -7.41 8.00e+00 1cpcA 162 -28.56 -7.34 8.49e+00 1g8jA 825 -32.06 -7.25 9.15e+00 1qpbA 563 -30.55 -7.21 9.43e+00 1g8kA 825 -32.06 -7.20 9.49e+00 1nmtA 392 -29.22 -7.19 9.59e+00 1cgo 127 -27.88 -7.09 1.04e+01 1jp3A 253 -30.96 -7.04 1.07e+01 1f44A 324 -31.75 -7.04 1.08e+01 1pvdA 537 -30.73 -7.04 1.08e+01 1jraA 117 -29.08 -7.02 1.10e+01 1bouA 139 -27.35 -6.91 1.20e+01 1ihfA 99 -25.91 -6.90 1.20e+01 1k8eA 345 -28.99 -6.89 1.21e+01 1eu8A 409 -30.40 -6.88 1.22e+01 1i3dA 146 -27.09 -6.88 1.23e+01 1k3fA 253 -28.62 -6.87 1.23e+01 3cla 213 -27.66 -6.76 1.35e+01 1jfzA 154 -30.30 -6.75 1.36e+01 1fe8A 196 -27.67 -6.74 1.37e+01 1pydA 556 -30.07 -6.70 1.41e+01 1b4uA 139 -27.36 -6.68 1.43e+01 1efnB 152 -26.01 -6.59 1.55e+01 1jr8A 117 -29.51 -6.56 1.58e+01 1f7wA 144 -26.47 -6.47 1.70e+01 1pyaB 228 -28.09 -6.45 1.73e+01 1crxA 322 -31.12 -6.40 1.80e+01 4crxA 322 -31.12 -6.40 1.81e+01 3crxA 343 -32.07 -6.40 1.81e+01 1kbuA 349 -31.87 -6.38 1.83e+01 1phnB 172 -27.87 -6.36 1.86e+01 1lox 662 -29.66 -6.36 1.86e+01 1k2yX 463 -30.88 -6.31 1.94e+01 1pjcA 361 -28.28 -6.25 2.03e+01 1shcA 195 -26.04 -6.17 2.18e+01 1sayA 361 -28.28 -6.16 2.18e+01 1aba 87 -23.96 -6.16 2.18e+01 1h99A 224 -28.60 -6.14 2.22e+01 1eexA 554 -28.54 -6.12 2.25e+01 1ej3A 191 -27.85 -6.12 2.25e+01 1whsA 255 -27.03 -6.10 2.30e+01 1ppa 121 -26.14 -6.09 2.32e+01 1pjbA 361 -28.33 -6.03 2.43e+01 1cnt2 187 -28.87 -6.02 2.45e+01 1kvoA 124 -27.28 -5.99 2.51e+01 1ax0 239 -26.48 -5.99 2.51e+01 1ar0A 127 -25.74 -5.98 2.52e+01 1hruA 188 -27.45 -5.95 2.58e+01 1dvbA 191 -29.20 -5.90 2.70e+01 1hv9A 456 -28.74 -5.87 2.78e+01 1aokB 122 -25.53 -5.86 2.78e+01 1dioA 554 -28.36 -5.86 2.80e+01 1ghr 306 -30.17 -5.85 2.81e+01 1e85A 127 -26.56 -5.85 2.82e+01 1cec 343 -30.32 -5.85 2.82e+01 1ah6 220 -26.68 -5.83 2.86e+01 1dklA 410 -27.90 -5.81 2.90e+01 1ip9A 85 -23.60 -5.80 2.94e+01 1fwyA 331 -28.39 -5.79 2.97e+01 1alq 266 -27.76 -5.77 3.00e+01 2hmiA 558 -32.09 -5.76 3.02e+01 1gv3A 248 -28.01 -5.74 3.08e+01 1tfe 145 -26.82 -5.74 3.09e+01 1whtA 256 -26.81 -5.73 3.11e+01 1klqA 197 -31.14 -5.72 3.13e+01 1yuiA 54 -21.68 -5.72 3.14e+01 1itxA 419 -29.43 -5.69 3.21e+01 1ii5A 233 -27.81 -5.68 3.24e+01 1fxjA 331 -28.42 -5.67 3.25e+01 1aw5 326 -30.12 -5.67 3.26e+01 1bcsA 263 -26.67 -5.65 3.31e+01 1efuB 282 -28.77 -5.65 3.32e+01 1gzcA 239 -26.50 -5.64 3.35e+01 1d0qA 103 -25.09 -5.63 3.36e+01 1dkqA 410 -27.77 -5.62 3.38e+01 1ceo 343 -30.11 -5.62 3.39e+01 1jltB 122 -25.42 -5.57 3.53e+01 1bvsB 203 -25.88 -5.56 3.57e+01 1iiwA 232 -27.66 -5.56 3.58e+01 1iso 416 -29.06 -5.54 3.64e+01 1fztA 211 -26.62 -5.53 3.65e+01 1bed 181 -28.37 -5.52 3.67e+01 1f47B 144 -25.71 -5.52 3.68e+01 1atzB 189 -26.32 -5.48 3.80e+01 1xsm 390 -31.07 -5.46 3.88e+01 1bgp 309 -28.59 -5.46 3.88e+01 1ounA 127 -25.38 -5.43 3.96e+01 1f7tA 122 -24.71 -5.43 3.96e+01 7icd 416 -28.75 -5.42 3.99e+01