% 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. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YGR041W.t2k-100-30-dssp-ehl2 Host: cc42 Tue Nov 12 04:59:32 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-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 548 nodes, 373.06 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(=1.5367) * Reverse)^tau(=0.7770))) % 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 1xsoA 150 -33.06 -10.71 1.09e+00 1qgtA 149 -30.50 -9.89 1.84e+00 8fabB 224 -32.77 -8.98 3.35e+00 1yghA 164 -29.27 -8.63 4.24e+00 1jj2A 239 -34.58 -8.48 4.67e+00 2cba 260 -33.44 -8.25 5.49e+00 1caj 260 -33.22 -8.02 6.39e+00 1ikoP 178 -32.44 -7.87 7.07e+00 1igrA 478 -34.89 -7.79 7.51e+00 1nls 237 -32.50 -7.73 7.83e+00 1tgoA 773 -33.45 -7.68 8.11e+00 2cab 261 -33.26 -7.60 8.53e+00 1hcb 260 -33.48 -7.54 8.91e+00 1thv 207 -29.72 -7.52 9.04e+00 1c9kB 180 -28.60 -7.42 9.65e+00 1scs 237 -32.28 -7.41 9.74e+00 1fr7A 260 -32.31 -7.37 1.00e+01 1thw 207 -29.83 -7.29 1.06e+01 1heuA 374 -32.06 -7.20 1.12e+01 1kxlA 199 -31.82 -7.08 1.22e+01 1jh6A 189 -27.91 -7.04 1.26e+01 1fsiA 189 -28.13 -7.03 1.27e+01 1hetA 374 -31.81 -6.96 1.33e+01 1h7zA 194 -30.86 -6.88 1.41e+01 1iwgA 1053 -33.92 -6.80 1.49e+01 1jqpA 438 -32.55 -6.72 1.58e+01 1fsu 492 -34.61 -6.71 1.59e+01 1ejfA 125 -28.24 -6.67 1.64e+01 1sur 215 -28.05 -6.58 1.75e+01 1cbuA 180 -28.02 -6.57 1.75e+01 1kwhA 492 -30.42 -6.49 1.86e+01 1iw7C 1119 -37.15 -6.44 1.92e+01 1sva1 361 -37.69 -6.34 2.07e+01 1bn8A 420 -31.94 -6.33 2.09e+01 2thiA 379 -31.28 -6.32 2.11e+01 2ohxA 374 -31.68 -6.29 2.14e+01 1c9kA 180 -28.31 -6.29 2.14e+01 1qcrA 446 -29.92 -6.26 2.19e+01 1ab4 477 -31.42 -6.26 2.20e+01 1hurA 180 -29.34 -6.25 2.21e+01 1dmlA 319 -29.86 -6.23 2.25e+01 1fzaB 328 -32.89 -6.22 2.25e+01 1jb9A 316 -32.18 -6.21 2.27e+01 8adh 374 -31.55 -6.20 2.29e+01 2stv 195 -27.83 -6.19 2.31e+01 1earA 147 -26.83 -6.16 2.36e+01 1eb0A 147 -26.91 -6.16 2.36e+01 1r2fA 319 -28.66 -6.14 2.39e+01 2at2A 300 -32.13 -5.99 2.66e+01 1thjA 214 -30.02 -5.96 2.72e+01 1gweA 503 -31.84 -5.95 2.75e+01 1hbzA 498 -31.53 -5.93 2.79e+01 2ltnA 181 -31.30 -5.92 2.80e+01 1at3A 247 -30.07 -5.90 2.84e+01 1eh9A 558 -35.99 -5.80 3.07e+01 1eulA 994 -33.37 -5.73 3.23e+01 3thiA 371 -30.44 -5.67 3.36e+01 1ee2A 373 -30.67 -5.62 3.49e+01 1kf6D 119 -30.07 -5.59 3.57e+01 1lktA 104 -26.62 -5.57 3.63e+01 1et7A 341 -29.97 -5.52 3.75e+01 1nfdA 203 -29.00 -5.48 3.88e+01 2fcr 173 -27.75 -5.47 3.90e+01 2phlA 397 -30.43 -5.46 3.92e+01 1dbuA 158 -26.86 -5.46 3.93e+01