% 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.YGR041W.t2k-100-30-stride-ebghtl Host: cc42 Tue Nov 12 04:46:44 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.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 YGR041W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR041W.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 548 nodes, 378.71 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(=1.4515) * Reverse)^tau(=0.7610))) % 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 -36.91 -12.90 6.73e-01 8fabB 224 -35.92 -10.87 2.10e+00 1nls 237 -34.93 -10.55 2.51e+00 1jj2A 239 -36.93 -10.51 2.57e+00 1qgtA 149 -31.59 -10.05 3.36e+00 1ikoP 178 -34.43 -9.48 4.68e+00 1fr7A 260 -33.27 -9.36 5.04e+00 2cba 260 -34.24 -9.34 5.09e+00 1scs 237 -32.81 -9.26 5.35e+00 1caj 260 -34.02 -9.20 5.54e+00 2fcr 173 -31.40 -8.47 8.59e+00 1igrA 478 -37.34 -8.45 8.67e+00 1bn8A 420 -34.31 -8.30 9.51e+00 1tgoA 773 -33.77 -8.10 1.07e+01 1amm 174 -28.90 -8.00 1.14e+01 1pbwA 216 -30.10 -7.88 1.22e+01 1fsu 492 -35.59 -7.87 1.23e+01 1c9kB 180 -29.09 -7.84 1.26e+01 1c9kA 180 -29.21 -7.71 1.36e+01 1kf6D 119 -33.82 -7.58 1.48e+01 1fzaB 328 -35.94 -7.53 1.53e+01 4gcr 174 -28.27 -7.41 1.65e+01 2stv 195 -29.66 -7.38 1.68e+01 1hxxA 340 -31.25 -7.32 1.74e+01 1eb0A 147 -28.24 -7.29 1.77e+01 1lktA 104 -29.29 -7.24 1.83e+01 1dbuA 158 -28.94 -7.23 1.85e+01 1dbxA 158 -28.94 -7.15 1.94e+01 1yghA 164 -28.06 -7.10 1.99e+01 1c8gA 548 -44.14 -7.07 2.03e+01 1r2fA 319 -30.80 -7.06 2.05e+01 1kekA 1231 -37.15 -7.00 2.12e+01 1as8A 343 -31.61 -6.99 2.14e+01 1j9qA 341 -31.47 -6.91 2.25e+01 1bjt 793 -32.79 -6.85 2.34e+01 1yge 839 -35.98 -6.83 2.36e+01 2omf 340 -30.73 -6.81 2.41e+01 1cbuA 180 -29.09 -6.80 2.41e+01 2thiA 379 -33.87 -6.78 2.44e+01 1ejfA 125 -28.79 -6.70 2.57e+01 1eh9A 558 -34.78 -6.65 2.67e+01 1thw 207 -29.71 -6.61 2.72e+01 1nfdA 203 -31.20 -6.61 2.73e+01 1dmlA 319 -29.88 -6.58 2.77e+01 1thv 207 -29.45 -6.58 2.78e+01 2cab 261 -32.55 -6.40 3.12e+01 1c5mD 255 -30.44 -6.39 3.14e+01 3rp2A 224 -30.34 -6.38 3.16e+01 1g2lA 235 -30.32 -6.36 3.19e+01 1d3cA 686 -32.79 -6.29 3.35e+01 1b4kA 337 -29.55 -6.28 3.37e+01 1earA 147 -27.10 -6.18 3.60e+01 1sur 215 -27.54 -6.13 3.71e+01 1fjsA 234 -29.98 -6.13 3.73e+01 1h7zA 194 -33.72 -6.11 3.77e+01 2cb5A 453 -29.89 -6.08 3.83e+01 1bd2D 204 -30.81 -6.07 3.86e+01 1jtaA 361 -31.32 -6.03 3.96e+01