% 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.YGR025W.t2k-100-30-str Host: cc47 Fri Nov 8 17:38:25 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.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 YGR025W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR025W.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7310 sequences, 1706072 residues, 101 nodes, 67.79 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(=2.3624) * Reverse)^tau(=0.7242))) % 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 1ddt 535 -30.79 -9.13 7.07e-01 1dfnA 30 -22.86 -7.57 2.29e+00 1f0lA 535 -29.03 -7.45 2.50e+00 1irk 306 -26.57 -6.63 4.76e+00 1jenA 267 -27.65 -6.49 5.35e+00 1iqaA 160 -26.67 -6.48 5.40e+00 1eaiC 61 -25.65 -6.40 5.75e+00 1i2hA 168 -26.60 -6.38 5.83e+00 1j6nA 303 -24.92 -6.33 6.08e+00 1slvA 142 -29.03 -6.23 6.62e+00 1je5A 206 -27.11 -6.03 7.75e+00 1qppA 218 -27.44 -6.00 7.95e+00 1mak 113 -25.24 -5.92 8.52e+00 1ddwA 120 -25.25 -5.91 8.60e+00 1sluA 142 -29.09 -5.84 9.09e+00 1b9wA 89 -24.92 -5.80 9.36e+00 1ir3A 306 -25.67 -5.77 9.67e+00 1ihgA 370 -27.91 -5.76 9.74e+00 1jpaA 312 -26.23 -5.61 1.10e+01 1nglA 179 -27.97 -5.33 1.40e+01 1sva1 361 -27.75 -5.28 1.46e+01 1ddvA 111 -25.82 -5.22 1.53e+01 1g0sA 209 -25.64 -5.18 1.58e+01 1icfA 175 -24.83 -5.12 1.67e+01 1jroB 777 -27.81 -5.03 1.80e+01 1fthA 122 -22.85 -4.92 1.99e+01 1a1z 91 -20.45 -4.83 2.15e+01 1pdgC 109 -27.49 -4.79 2.21e+01 1b65A 375 -26.61 -4.74 2.32e+01 1cz3A 168 -23.62 -4.56 2.71e+01 1am2 199 -24.50 -4.54 2.77e+01 1d2oA 187 -24.95 -4.54 2.77e+01 1a1w 91 -20.10 -4.51 2.83e+01 1lba 146 -22.08 -4.48 2.91e+01 1ib8A 164 -23.93 -4.47 2.94e+01 1cs8A 316 -25.53 -4.44 3.02e+01 1bbt3 220 -25.27 -4.41 3.09e+01 1pdgA 109 -28.29 -4.41 3.09e+01 1d2pA 373 -26.38 -4.39 3.16e+01 1qqp3 220 -25.15 -4.32 3.38e+01 1a3lL 217 -25.26 -4.30 3.41e+01 1dokA 77 -22.38 -4.30 3.42e+01 1dfaA 454 -26.87 -4.30 3.43e+01 1bj7 156 -25.24 -4.29 3.44e+01 1xbrA 184 -24.74 -4.26 3.57e+01 1d1gA 168 -23.20 -4.21 3.71e+01 1dlfL 113 -22.97 -4.20 3.74e+01 1al0G 175 -25.39 -4.20 3.76e+01 1qmeA 702 -26.42 -4.18 3.81e+01 1eagA 342 -25.55 -4.16 3.90e+01 1jb9A 316 -25.76 -4.15 3.93e+01