% 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. % --------------------------------------------------------------------- % w0.5foo.1.YGR016W.t2k-w0.5.mod Host: cc41 Fri Nov 8 16:52:23 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR016W % --------------------------------------------------------------------- % Inserted Files: YGR016W.t2k-w0.5.mod % Database Files: /projects/compbio/experiments/protein-predict/SAM_T02/data/pdbaa % % 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)) % Single Track Model: YGR016W.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13975 sequences, 3107935 residues, 191 nodes, 188.78 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(=2.9337) * Reverse)^tau(=0.7348))) % 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 1cqa 133 -26.94 -7.91 3.06e-01 1g5iD 454 -27.63 -5.59 2.97e+00 1g5hA 454 -27.48 -5.43 3.49e+00 1e50B 134 -23.30 -5.03 5.34e+00 1h9dB 134 -23.30 -5.03 5.34e+00 1cl3A 138 -23.25 -4.80 6.75e+00 1yasA 257 -24.71 -4.80 6.77e+00 1qj4A 257 -24.71 -4.80 6.77e+00 1ilfA 141 -23.27 -4.79 6.84e+00 1eboA 131 -23.67 -4.79 6.86e+00 2jhbA 143 -23.28 -4.78 6.91e+00 1outA 143 -23.44 -4.68 7.68e+00 1efeA 60 -20.87 -4.49 9.50e+00 1ko4A 175 -24.36 -4.47 9.63e+00 1gn2A 207 -24.92 -4.43 1.01e+01 1em1A 198 -24.20 -4.40 1.04e+01 1luwA 198 -24.00 -4.18 1.33e+01 1ja8A 198 -23.97 -4.16 1.36e+01 1abmA 198 -23.97 -4.15 1.38e+01 1ezvE 185 -23.69 -4.12 1.42e+01 1lv9A 77 -21.18 -4.11 1.44e+01 1qnmA 198 -23.90 -4.10 1.46e+01 1ap6A 198 -23.90 -4.08 1.48e+01 1lusA 198 -23.90 -4.08 1.49e+01 1spgA 144 -23.44 -4.06 1.53e+01 1aat 411 -24.68 -3.98 1.66e+01 1varA 198 -23.89 -3.97 1.68e+01 1ct8B 220 -23.24 -3.92 1.78e+01 2cstA 411 -24.66 -3.91 1.80e+01 2eboA 74 -21.05 -3.88 1.87e+01 2mllA 241 -23.95 -3.79 2.07e+01 1ce7A 241 -23.95 -3.77 2.09e+01 1af5 126 -22.13 -3.70 2.29e+01 1aw5 326 -24.55 -3.67 2.35e+01 1eqrA 590 -25.56 -3.67 2.36e+01 1c0aA 585 -25.55 -3.67 2.37e+01 1afvH 220 -22.87 -3.64 2.45e+01 1m56A 566 -26.52 -3.53 2.76e+01 1m57A 566 -26.51 -3.53 2.78e+01 1dceA 567 -25.11 -3.53 2.78e+01 1qsdA 106 -21.72 -3.51 2.85e+01 1vpu 45 -20.33 -3.50 2.89e+01 1g5uA 131 -22.50 -3.49 2.91e+01 1i6uA 130 -21.88 -3.48 2.92e+01 1kkqA 269 -24.20 -3.48 2.94e+01 1qklA 127 -22.60 -3.46 3.00e+01 1knqA 175 -23.19 -3.44 3.07e+01 1k7lA 288 -24.28 -3.44 3.09e+01 1cp2A 269 -23.92 -3.43 3.11e+01 1civA 385 -24.58 -3.42 3.13e+01 1c8m2 252 -23.76 -3.40 3.23e+01 1i7gA 287 -24.27 -3.40 3.24e+01 1fnlA 175 -22.54 -3.39 3.26e+01 1hskA 326 -24.29 -3.39 3.26e+01 1e4kC 176 -22.54 -3.38 3.29e+01 1iisC 176 -22.54 -3.38 3.29e+01 1kwpA 400 -24.58 -3.37 3.33e+01 1dfkA 830 -26.16 -3.30 3.63e+01 1dflA 831 -26.16 -3.30 3.64e+01 1b7tA 835 -26.17 -3.29 3.65e+01 1aym2 261 -23.79 -3.25 3.85e+01 1tih 53 -19.37 -3.23 3.92e+01