% 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. % --------------------------------------------------------------------- % strfoo.1.YGR235C.t2k-100-30-str Host: cc86 Tue Nov 12 18:45:49 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR235C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.strs % % 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 YGR235C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR235C.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 234 nodes, 157.05 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(=1.9477) * Reverse)^tau(=0.7451))) % 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 1iwhB 146 -33.83 -12.95 1.13e-01 1iq0A 592 -35.66 -12.95 1.13e-01 2olbA 517 -34.90 -11.98 2.11e-01 1jevA 517 -34.95 -11.91 2.21e-01 1jetA 517 -34.54 -11.58 2.75e-01 1sig 339 -34.65 -11.42 3.05e-01 1ass 159 -31.87 -10.09 7.41e-01 1kl7A 514 -33.03 -9.38 1.20e+00 1g0u1 266 -30.74 -9.25 1.32e+00 1fliA 98 -28.19 -9.23 1.33e+00 1asx 159 -30.88 -9.00 1.57e+00 1dxtB 147 -30.11 -8.49 2.24e+00 1babB 146 -30.09 -8.49 2.26e+00 1ryp2 233 -29.70 -8.32 2.54e+00 1fhjB 146 -30.74 -8.17 2.82e+00 1eupA 403 -33.37 -8.14 2.89e+00 1irdB 146 -28.77 -7.83 3.61e+00 1mgtA 174 -28.46 -7.18 5.81e+00 1ib8A 164 -26.75 -7.10 6.16e+00 1spgB 147 -28.18 -6.95 6.87e+00 1yme 309 -27.85 -6.91 7.08e+00 1j5eC 239 -27.32 -6.85 7.41e+00 1fjgC 239 -27.09 -6.76 7.91e+00 1oxa 403 -31.88 -6.70 8.33e+00 1cyo 93 -24.28 -6.67 8.48e+00 2ctb 307 -27.67 -6.63 8.73e+00 1hu4A 288 -28.48 -6.50 9.69e+00 1hw5A 210 -27.28 -6.34 1.09e+01 1jenA 267 -26.99 -6.33 1.10e+01 1im4A 221 -27.03 -6.26 1.16e+01 1hcnA 92 -24.97 -6.26 1.16e+01 1cem 363 -28.61 -6.22 1.20e+01 1i3dA 146 -28.50 -6.19 1.23e+01 1kwfA 363 -28.66 -6.17 1.24e+01 1j54A 186 -26.11 -6.17 1.24e+01 1jx4A 352 -30.31 -6.11 1.30e+01 1a99A 344 -27.70 -6.08 1.33e+01 1ajsA 412 -29.03 -6.06 1.36e+01 1lucB 324 -27.54 -6.01 1.41e+01 1im5A 180 -25.99 -5.96 1.46e+01 1i0hA 205 -29.58 -5.91 1.52e+01 1gd5A 130 -26.69 -5.90 1.53e+01 1ci8A 392 -27.74 -5.85 1.59e+01 2ctc 307 -26.80 -5.81 1.64e+01 1dz7A 92 -23.61 -5.80 1.65e+01 6cpa 307 -26.57 -5.77 1.70e+01 2cgpA 210 -26.33 -5.76 1.71e+01 1brlB 324 -27.26 -5.74 1.74e+01 1ci9A 392 -27.69 -5.74 1.74e+01 1in6A 334 -27.77 -5.66 1.85e+01 1amk 251 -26.89 -5.65 1.86e+01 1fqvJ 149 -26.32 -5.62 1.91e+01 1fqvD 149 -26.27 -5.54 2.02e+01 1jl0A 334 -26.44 -5.48 2.12e+01 1cot 129 -24.53 -5.45 2.18e+01 1lqxA 82 -22.78 -5.39 2.29e+01 1ap6A 198 -26.79 -5.39 2.29e+01 1fjgR 88 -24.43 -5.37 2.33e+01 1k8kA 418 -28.33 -5.36 2.34e+01 1blu 82 -23.59 -5.35 2.37e+01 1g7dA 106 -27.13 -5.33 2.40e+01 1aisB 200 -26.36 -5.32 2.43e+01 1lla 628 -30.39 -5.31 2.43e+01 1abmA 198 -26.79 -5.31 2.43e+01 1d5nA 205 -28.99 -5.24 2.58e+01 1jkiA 533 -27.86 -5.21 2.64e+01 1cojA 212 -27.77 -5.12 2.83e+01 1bob 320 -26.87 -5.12 2.84e+01 2spcA 107 -26.88 -5.12 2.85e+01 1jipA 403 -29.69 -5.11 2.85e+01 1sur 215 -26.42 -5.08 2.93e+01 1fqiA 147 -26.98 -5.07 2.95e+01 1lfpA 249 -26.43 -5.00 3.12e+01 1g13A 162 -23.83 -4.96 3.22e+01 1a6dA 545 -33.24 -4.95 3.26e+01 1lrzA 426 -28.47 -4.88 3.45e+01 1e5eA 404 -27.52 -4.85 3.52e+01 1udh 244 -26.10 -4.85 3.53e+01 1tsm 316 -26.41 -4.84 3.57e+01 3pghA 587 -28.22 -4.80 3.68e+01 1h5wA 309 -27.79 -4.79 3.69e+01 1e9lA 377 -26.20 -4.79 3.70e+01 7icd 416 -27.69 -4.75 3.83e+01 1udg 244 -25.96 -4.73 3.89e+01 1csn 298 -27.46 -4.73 3.91e+01 1kewA 361 -26.56 -4.71 3.96e+01