% 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. % --------------------------------------------------------------------- % dsspfoo.1.YGR041W.t2k-100-30-dssp-ebghstl Host: cc42 Tue Nov 12 04:40:29 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR041W % --------------------------------------------------------------------- % 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 ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR041W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR041W.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 548 nodes, 373.24 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(=1.6300) * Reverse)^tau(=0.7739))) % 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 1tgoA 773 -38.46 -12.47 2.49e-01 1h7zA 194 -35.28 -10.35 9.94e-01 1xsoA 150 -33.64 -10.34 1.00e+00 1qgtA 149 -30.93 -10.19 1.10e+00 8fabB 224 -33.47 -10.16 1.12e+00 2cba 260 -34.02 -9.59 1.65e+00 1nls 237 -32.88 -9.49 1.77e+00 1caj 260 -33.75 -9.34 1.96e+00 1scs 237 -32.74 -9.33 1.97e+00 1fsu 492 -35.91 -9.24 2.10e+00 1c9kB 180 -29.64 -8.89 2.66e+00 1jj2A 239 -33.23 -8.17 4.40e+00 1c9kA 180 -29.36 -8.12 4.57e+00 1ey2A 471 -35.54 -7.93 5.21e+00 1cbuA 180 -29.30 -7.77 5.85e+00 2stv 195 -29.49 -7.73 5.99e+00 1eulA 994 -35.32 -7.60 6.58e+00 3thiA 371 -32.27 -7.53 6.91e+00 1fr7A 260 -31.63 -7.52 6.99e+00 1nfdA 203 -30.53 -7.44 7.39e+00 2thiA 379 -32.15 -7.41 7.54e+00 1igrA 478 -33.47 -7.40 7.59e+00 1klt 226 -32.01 -7.38 7.71e+00 1hcb 260 -34.48 -7.35 7.90e+00 1ikoP 178 -31.62 -7.32 8.08e+00 2fcr 173 -30.47 -7.26 8.40e+00 2ltnA 181 -31.23 -7.24 8.53e+00 2cab 261 -33.39 -7.20 8.75e+00 1lktA 104 -28.42 -7.11 9.38e+00 1yghA 164 -27.57 -7.03 9.89e+00 1kv7A 488 -32.40 -6.97 1.03e+01 1jb9A 316 -34.38 -6.97 1.04e+01 1pbwA 216 -28.79 -6.97 1.04e+01 1dboA 506 -34.65 -6.91 1.08e+01 1iwgA 1053 -33.87 -6.89 1.10e+01 1kf6D 119 -31.65 -6.80 1.17e+01 1dkiA 371 -34.60 -6.76 1.21e+01 1eonA 245 -29.57 -6.72 1.24e+01 1jhnA 424 -41.90 -6.68 1.28e+01 1eybA 471 -35.64 -6.67 1.29e+01 1dbuA 158 -27.63 -6.57 1.39e+01 1hjp 203 -27.14 -6.47 1.50e+01 2cas 548 -40.35 -6.46 1.50e+01 1m0kA 262 -31.06 -6.44 1.53e+01 1dbxA 158 -27.55 -6.40 1.58e+01 1thw 207 -28.17 -6.35 1.63e+01 1thv 207 -28.16 -6.31 1.69e+01 4dpvZ 584 -39.45 -6.21 1.81e+01 1yge 839 -35.69 -6.14 1.91e+01 1eh9A 558 -35.30 -6.06 2.03e+01 3rp2A 224 -28.79 -6.05 2.04e+01 1dyr 206 -27.60 -6.05 2.04e+01 1rthA 560 -32.37 -6.05 2.05e+01 1sur 215 -27.06 -6.01 2.11e+01 1al0F 426 -31.92 -6.00 2.12e+01 1b4kA 337 -29.36 -5.99 2.13e+01 1vrtA 560 -32.60 -5.95 2.20e+01 1r2fA 319 -28.63 -5.95 2.20e+01 1eq3A 96 -26.02 -5.89 2.30e+01 2at2A 300 -32.79 -5.88 2.32e+01 1kekA 1231 -34.94 -5.85 2.37e+01 1hetA 374 -30.42 -5.83 2.41e+01 1qfeA 252 -27.40 -5.83 2.41e+01 2ercA 244 -28.72 -5.80 2.46e+01 1c3wA 222 -29.36 -5.74 2.59e+01 1dbgA 506 -33.34 -5.71 2.64e+01 1htrB 329 -29.40 -5.65 2.77e+01 1b0pA 1231 -34.76 -5.63 2.80e+01 1heuA 374 -30.22 -5.63 2.80e+01 1bvoA 175 -30.14 -5.61 2.84e+01 1earA 147 -26.12 -5.61 2.85e+01 1fzaB 328 -32.66 -5.56 2.95e+01 1ffkC 246 -31.20 -5.56 2.96e+01 1qcrA 446 -29.26 -5.56 2.97e+01 1ehaA 558 -35.42 -5.54 3.01e+01 1i52A 236 -26.98 -5.52 3.04e+01 1hurA 180 -28.12 -5.52 3.05e+01 1thjA 214 -28.44 -5.52 3.06e+01 1fiqC 763 -31.25 -5.51 3.06e+01 1f8nA 839 -34.95 -5.48 3.15e+01 1bdmA 327 -27.66 -5.48 3.16e+01 1eb0A 147 -26.13 -5.47 3.17e+01 1bmdA 327 -27.66 -5.43 3.27e+01 1fyc 106 -27.64 -5.36 3.44e+01 1gzgA 337 -28.62 -5.36 3.45e+01 1gpc 218 -27.50 -5.35 3.48e+01 2ohxA 374 -30.24 -5.32 3.57e+01 1jgsA 138 -27.24 -5.31 3.58e+01 1kxlA 199 -29.47 -5.28 3.66e+01 1hbzA 498 -32.08 -5.27 3.69e+01 1tx4A 198 -26.28 -5.26 3.72e+01 1jh6A 189 -25.57 -5.26 3.74e+01 1goh 639 -33.86 -5.25 3.76e+01 1j54A 186 -25.83 -5.24 3.79e+01 1k3iA 656 -34.40 -5.23 3.81e+01 1et7A 341 -28.96 -5.21 3.87e+01 1kwhA 492 -31.86 -5.21 3.87e+01 1hm6A 346 -27.29 -5.19 3.94e+01 1qd1A 325 -27.56 -5.18 3.95e+01