% 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.YGR022C.t2k-100-30-stride-ebghtl Host: cc51 Fri Nov 8 17:22:10 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR022C % --------------------------------------------------------------------- % 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 YGR022C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR022C.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7310 sequences, 1706072 residues, 110 nodes, 73.90 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(=2.3707) * Reverse)^tau(=0.7600))) % 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 1in6A 334 -30.55 -9.94 1.17e-01 1in4A 334 -29.65 -8.99 2.65e-01 1gpmA 525 -29.94 -7.63 8.76e-01 1faaA 124 -25.09 -7.38 1.10e+00 1grj 158 -26.80 -6.42 2.67e+00 1kk1A 410 -27.54 -6.10 3.60e+00 1d3bB 91 -22.80 -5.83 4.65e+00 1pot 325 -26.30 -5.73 5.13e+00 1l0wA 580 -27.70 -5.64 5.58e+00 1nddD 76 -22.61 -5.48 6.54e+00 1c7nA 399 -26.04 -5.44 6.76e+00 1nddA 76 -22.53 -5.42 6.93e+00 1d0yA 761 -27.75 -5.34 7.48e+00 1c0pA 363 -26.28 -5.33 7.58e+00 1fts 295 -25.82 -5.30 7.75e+00 1bt0A 76 -22.32 -5.27 8.05e+00 1ykfA 352 -26.61 -5.25 8.14e+00 1gzgA 337 -25.57 -5.17 8.80e+00 1b4kA 337 -25.52 -5.12 9.33e+00 1lvk 762 -27.73 -5.10 9.44e+00 1mpgA 282 -24.71 -4.90 1.16e+01 1acc 735 -26.56 -4.84 1.23e+01 1mnd 762 -27.22 -4.81 1.26e+01 1j83A 180 -23.58 -4.80 1.28e+01 1vom 762 -27.07 -4.72 1.38e+01 1qs2A 401 -25.37 -4.59 1.58e+01 1knt 58 -20.42 -4.59 1.59e+01 1kthA 58 -20.40 -4.58 1.60e+01 2knt 58 -20.40 -4.58 1.60e+01 1qe3A 489 -25.46 -4.53 1.67e+01 1jjyA 636 -28.19 -4.43 1.86e+01 1fb6A 105 -22.94 -4.42 1.87e+01 1cjwA 166 -22.98 -4.39 1.94e+01 1thx 115 -22.29 -4.33 2.07e+01 1jndA 420 -25.36 -4.31 2.11e+01 1rcb 129 -22.06 -4.16 2.45e+01 1cjcA 460 -24.93 -4.16 2.46e+01 2int 129 -22.06 -4.16 2.46e+01 1itm 130 -22.09 -4.11 2.58e+01 1cnzA 363 -25.70 -4.08 2.68e+01 1hziA 129 -22.06 -4.07 2.71e+01 1e8cA 498 -25.79 -4.06 2.72e+01 1kevA 351 -25.85 -4.05 2.76e+01 1ju2A 536 -26.28 -3.95 3.07e+01 1b2pA 119 -21.94 -3.95 3.07e+01 3grs 478 -25.09 -3.92 3.16e+01 4gr1 478 -25.09 -3.91 3.18e+01 1evsA 187 -23.50 -3.90 3.22e+01 1i9bA 217 -23.17 -3.88 3.28e+01 1gfsA 321 -24.17 -3.85 3.40e+01 1bsvA 321 -24.16 -3.82 3.51e+01 1iiwA 232 -23.84 -3.79 3.60e+01 3sicI 107 -21.90 -3.79 3.62e+01 1kuxA 207 -22.91 -3.76 3.74e+01 1auyA 189 -22.15 -3.75 3.79e+01