% 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. % --------------------------------------------------------------------- % alphafoo.1.YGR025W.t2k-100-30-alpha Host: cc47 Fri Nov 8 17:45:18 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR025W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.alphas % % 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 YGR025W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR025W.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7310 sequences, 1706072 residues, 101 nodes, 67.18 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(=3.1602) * Reverse)^tau(=0.7044))) % 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 1sluA 142 -26.82 -6.80 1.25e+00 1slvA 142 -26.57 -6.76 1.29e+00 1ihgA 370 -27.45 -6.68 1.39e+00 1eaiC 61 -24.91 -6.61 1.47e+00 1ddwA 120 -24.60 -6.51 1.62e+00 1ddvA 111 -24.60 -6.49 1.65e+00 1i2hA 168 -24.82 -6.16 2.24e+00 1ir3A 306 -25.10 -5.72 3.37e+00 1mak 113 -23.55 -5.70 3.42e+00 1nglA 179 -25.21 -5.53 4.03e+00 1irk 306 -24.88 -5.49 4.19e+00 1g0sA 209 -24.39 -5.39 4.60e+00 1f0lA 535 -26.68 -5.38 4.65e+00 1gio 125 -23.11 -5.34 4.82e+00 1qhxA 178 -23.41 -5.26 5.24e+00 1pdgC 109 -26.07 -5.14 5.91e+00 1jpaA 312 -24.74 -5.11 6.07e+00 1ddt 535 -25.97 -4.80 8.21e+00 1k59A 123 -23.23 -4.78 8.36e+00 1a4yB 123 -23.25 -4.75 8.61e+00 1iqaA 160 -23.46 -4.74 8.74e+00 1d2pA 373 -25.50 -4.72 8.86e+00 1pdgA 109 -25.54 -4.62 9.81e+00 1csn 298 -24.81 -4.61 9.91e+00 1d8cA 723 -26.34 -4.61 9.92e+00 1dfnA 30 -20.65 -4.58 1.02e+01 1am2 199 -23.38 -4.50 1.11e+01 1j6nA 303 -23.42 -4.48 1.13e+01 1e58A 249 -24.16 -4.47 1.14e+01 1jenA 267 -25.14 -4.47 1.15e+01 1qhsA 178 -22.58 -4.47 1.15e+01 1d2oA 187 -23.71 -4.43 1.19e+01 1hbyA 123 -23.08 -4.41 1.22e+01 1dlfL 113 -22.34 -4.39 1.25e+01 1a1z 91 -20.05 -4.32 1.33e+01 1hxmA 229 -25.46 -4.32 1.34e+01 1gr2A 279 -23.98 -4.31 1.35e+01 1rhd 293 -23.60 -4.31 1.35e+01 1qubA 319 -28.45 -4.29 1.38e+01 1k47A 337 -24.03 -4.24 1.45e+01 1a1w 91 -19.91 -4.22 1.47e+01 1itxA 419 -24.89 -4.16 1.58e+01 1je5A 206 -23.50 -4.11 1.66e+01 1b9wA 89 -21.46 -4.08 1.70e+01 1ftkA 279 -23.72 -4.08 1.72e+01 1jroB 777 -26.46 -4.06 1.74e+01 1agi 125 -21.86 -3.98 1.89e+01 1nra 63 -20.52 -3.96 1.94e+01 1rhs 296 -23.13 -3.89 2.08e+01 1qppA 218 -24.31 -3.89 2.09e+01 1lba 146 -21.97 -3.88 2.12e+01 2cpl 165 -25.68 -3.85 2.18e+01 1a44 185 -22.73 -3.84 2.19e+01 1h9oA 112 -21.36 -3.84 2.20e+01 1thg 544 -25.71 -3.84 2.21e+01 1d2vC 466 -24.78 -3.84 2.21e+01 1mhlC 466 -24.75 -3.74 2.46e+01 1gk8I 140 -22.49 -3.72 2.51e+01 1aym1 285 -23.84 -3.71 2.54e+01 1cp3A 277 -23.56 -3.70 2.56e+01 1cxpC 466 -24.62 -3.67 2.65e+01 1bj7 156 -23.26 -3.65 2.71e+01 1d3gA 367 -23.37 -3.64 2.73e+01 1jj2I 145 -21.29 -3.62 2.80e+01 1ibzA 112 -22.85 -3.57 2.94e+01 1cd9B 215 -23.30 -3.57 2.94e+01 1avgI 142 -22.79 -3.55 3.01e+01 1apyB 141 -21.31 -3.52 3.11e+01 1cwoA 165 -25.70 -3.49 3.20e+01 1awqA 164 -25.64 -3.48 3.25e+01 1qadA 111 -20.91 -3.38 3.64e+01 1a2vA 655 -26.70 -3.33 3.84e+01 1ibyA 112 -22.68 -3.32 3.85e+01 2rmcA 182 -23.34 -3.32 3.89e+01 1ei5A 520 -24.19 -3.31 3.89e+01