% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (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-T2K, 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, et al., What is the value added by human intervention in protein % structure prediction, Proteins: Stucture, Function, Genetics 45(S5):86--91, 2001. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % stridefoo.1.YGR034W.t2k-100-30-stride-ebghtl Host: farm20 Wed Nov 17 18:51:50 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR034W % --------------------------------------------------------------------- % 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 +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR034W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR034W.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10772 sequences, 2550165 residues, 130 nodes, 139.65 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 (=10700) sequences: % N / (1 + exp(-(lambda(=1.7582) * Reverse)^tau(=0.7246))) % 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 1s72T 120 -110.17 -95.83 1.57e-14 1jj2S 119 -109.67 -95.32 1.84e-14 1ffkQ 119 -103.49 -90.04 9.64e-14 1irp 153 -22.63 -10.88 2.21e+00 1bmfA 510 -21.84 -10.16 3.32e+00 1ilr1 152 -20.87 -10.15 3.34e+00 1dynA 125 -20.45 -10.08 3.48e+00 1iraX 152 -20.92 -10.07 3.50e+00 1az9 457 -20.05 -9.88 3.91e+00 1qa7B 217 -22.12 -9.87 3.94e+00 1qa7A 217 -21.52 -9.80 4.10e+00 1a16 440 -20.09 -9.78 4.15e+00 1x8mA 288 -22.05 -9.74 4.25e+00 1e32A 458 -21.95 -9.24 5.68e+00 1qmyA 167 -21.04 -9.09 6.20e+00 1bbzA 58 -18.63 -8.98 6.64e+00 1aboA 62 -18.60 -8.98 6.65e+00 1bbzE 58 -18.60 -8.97 6.66e+00 2dynA 122 -19.64 -8.84 7.20e+00 1h8eA 510 -20.23 -8.77 7.54e+00 1hlcA 129 -20.70 -8.74 7.65e+00 1rl6A 177 -23.24 -8.58 8.44e+00 1vie 62 -18.45 -8.46 9.06e+00 1vif 62 -18.45 -8.46 9.06e+00 1nhp 447 -18.59 -8.43 9.21e+00 1nhs 447 -18.58 -8.33 9.80e+00 1ejfA 125 -21.17 -8.23 1.04e+01 1njhA 119 -20.77 -8.09 1.14e+01 1mxgA 435 -18.74 -8.07 1.15e+01 1rhd 293 -16.77 -7.96 1.23e+01 1e79A 510 -19.06 -7.94 1.24e+01 1joa 447 -18.10 -7.88 1.29e+01 1ksiA 642 -21.46 -7.79 1.36e+01 1oxsC 353 -21.18 -7.61 1.53e+01 1oxxK 353 -21.18 -7.61 1.53e+01 1hf2A 210 -22.64 -7.58 1.56e+01 1a81A 254 -17.97 -7.54 1.59e+01 1i3zA 103 -18.15 -7.38 1.76e+01 1tueB 218 -19.44 -7.37 1.77e+01 1jhfA 202 -19.31 -7.34 1.81e+01 1m3sA 186 -16.12 -7.32 1.83e+01 1qhoA 686 -20.07 -7.28 1.88e+01 1g86A 142 -18.84 -7.28 1.88e+01 1ksiB 642 -21.46 -7.25 1.92e+01 1mek 120 -15.38 -7.20 1.98e+01 1i1jA 108 -18.11 -7.19 1.99e+01 1axiB 236 -19.36 -7.12 2.08e+01 1hdkA 141 -18.66 -7.11 2.10e+01 1bpr 191 -17.88 -7.09 2.12e+01 1qqhA 144 -19.19 -6.92 2.37e+01 1m2tA 254 -17.22 -6.92 2.37e+01 1hr0W 71 -16.71 -6.88 2.42e+01 1dkxA 219 -16.83 -6.84 2.48e+01 1dkzA 219 -16.73 -6.82 2.52e+01 1iwmA 186 -19.17 -6.74 2.65e+01 1l3aA 228 -15.99 -6.73 2.66e+01 1a49A 530 -19.01 -6.71 2.70e+01 1kypA 237 -19.88 -6.67 2.78e+01 1jgtA 513 -16.93 -6.65 2.81e+01 1lcl 142 -18.07 -6.59 2.91e+01 1tbgA 340 -17.61 -6.57 2.96e+01 1pbp 321 -16.42 -6.56 2.98e+01 1ixh 321 -16.42 -6.55 2.99e+01 1ema 236 -19.66 -6.55 3.00e+01 1pkn 530 -18.53 -6.55 3.00e+01 1a9xB 379 -19.10 -6.54 3.02e+01 1cl1A 395 -15.60 -6.51 3.07e+01 1d7qA 143 -17.58 -6.47 3.16e+01 1cl2A 395 -15.60 -6.46 3.17e+01 1fhoA 119 -16.99 -6.43 3.24e+01 1mrj 247 -16.31 -6.42 3.27e+01 1gotB 340 -17.59 -6.38 3.34e+01 1h2kA 349 -15.75 -6.37 3.37e+01 1h0hA 977 -16.54 -6.33 3.47e+01 1bjx 110 -15.13 -6.31 3.51e+01 2bjxA 110 -15.13 -6.31 3.51e+01 1u69A 163 -16.46 -6.29 3.55e+01 1f7sA 139 -15.42 -6.28 3.58e+01 1fcdA 401 -17.05 -6.25 3.65e+01 1mzeA 351 -15.74 -6.20 3.77e+01 3hhrB 203 -19.12 -6.20 3.78e+01 1um0A 365 -15.24 -6.18 3.81e+01 1pm4A 119 -20.71 -6.17 3.83e+01 1tuc 63 -16.81 -6.16 3.86e+01 1gpr 162 -17.56 -6.15 3.88e+01 1ii2A 524 -15.12 -6.15 3.89e+01 8fabA 212 -15.22 -6.14 3.93e+01 1nxzA 246 -15.84 -6.12 3.97e+01