%  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.
% ---------------------------------------------------------------------
%  dssp-ehl2foo.1.YGR016W.t2k-100-30-dssp-ehl2   Host: cc41    Fri Nov  8 17:14:57 2002
%  karplus                                       Dir:  /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR016W
% ---------------------------------------------------------------------
% Inserted Files: 
% Database Files:  /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.dssps
%
% 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 YGR016W.t2k-w0.5.mod
% Track 1 FIMs added (the generic node (5))
% Track 1 Coeff 0.300 File YGR016W.t2k.dssp-ehl2.mod
% Score DP Method: forward all-paths (dpstyle = 0)
% Align DP Method: viterbi (adpstyle = 1)
% 7310 sequences, 1706072 residues, 191 nodes, 127.51 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(=1.8487) * Reverse)^tau(=0.7743)))
%    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
1g5hA             454       -33.70      -10.58     3.34e-01
1yasA             257       -29.98       -9.18     9.45e-01
1qj4A             257       -29.22       -8.45     1.65e+00
1g99A             408       -29.72       -7.50     3.45e+00
1hnoA             280       -29.04       -7.03     5.01e+00
1b43A             340       -28.56       -6.86     5.75e+00
1hzpA             335       -27.64       -6.82     5.93e+00
1abmA             198       -27.63       -6.63     6.92e+00
1yprA             125       -26.74       -6.57     7.26e+00
1bmfA             510       -29.31       -6.57     7.26e+00
1ap6A             198       -27.39       -6.57     7.28e+00
1f00I             282       -26.65       -6.46     7.98e+00
1hnuA             280       -28.42       -6.17     1.01e+01
1ukz              203       -27.68       -6.07     1.10e+01
1howA             373       -28.00       -5.84     1.33e+01
1go5A              69       -23.92       -5.79     1.38e+01
1jenA             267       -26.77       -5.73     1.45e+01
1qklA             127       -25.22       -5.68     1.51e+01
1dofA             403       -28.64       -5.63     1.59e+01
1gwcA             230       -28.29       -5.51     1.75e+01
1eyeA             280       -26.76       -5.50     1.76e+01
1i7gA             287       -27.85       -5.47     1.81e+01
1fp1D             372       -28.28       -5.36     1.99e+01
1gv3A             248       -27.01       -5.17     2.33e+01
1knqA             175       -27.70       -5.12     2.45e+01
1lmb3              92       -23.38       -5.08     2.52e+01
1hv2A              99       -25.25       -5.02     2.65e+01
1a0k              131       -24.67       -4.92     2.90e+01
1awcA             110       -25.27       -4.81     3.19e+01
1lliA              92       -23.03       -4.81     3.20e+01
1jq4A              98       -23.21       -4.77     3.30e+01
1k8kA             418       -27.42       -4.75     3.36e+01
2eboA              74       -23.07       -4.72     3.45e+01
3nul              130       -24.50       -4.67     3.61e+01
1k3eA             156       -25.05       -4.57     3.94e+01