%  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.
% ---------------------------------------------------------------------
%  dsspfoo.1.YGR039W.t2k-100-30-dssp-ebghstl   Host: cc41    Fri Nov  8 19:44:31 2002
%  karplus                                     Dir:  /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR039W
% ---------------------------------------------------------------------
% 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 YGR039W.t2k-w0.5.mod
% Track 1 FIMs added (the generic node (5))
% Track 1 Coeff 0.300 File YGR039W.t2k.dssp-ebghstl.mod
% Score DP Method: forward all-paths (dpstyle = 0)
% Align DP Method: viterbi (adpstyle = 1)
% 7323 sequences, 1713023 residues, 104 nodes, 70.28 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(=2.1193) * Reverse)^tau(=0.7337)))
%    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
1h2eA             207       -27.10       -6.81     6.10e+00
1hf2A             210       -26.41       -6.56     7.39e+00
1ebbA             202       -26.71       -6.51     7.66e+00
1bhe              376       -26.58       -6.41     8.27e+00
1fjgB             256       -28.01       -6.25     9.39e+00
1j5eB             256       -27.80       -6.07     1.08e+01
1qczA             169       -27.20       -5.98     1.16e+01
1tmy              120       -25.68       -5.96     1.17e+01
1sfp              114       -23.88       -5.88     1.25e+01
1h4wA             224       -24.21       -5.47     1.75e+01
1c1kA             217       -26.64       -5.42     1.81e+01
1pmt              203       -25.15       -5.34     1.93e+01
1szt               68       -22.91       -5.32     1.97e+01
1pyp              285       -24.52       -5.15     2.26e+01
1jj7A             260       -26.22       -5.10     2.36e+01
1b4bA              71       -21.98       -5.08     2.39e+01
1hd2A             161       -24.21       -5.04     2.48e+01
1rtfB             252       -24.32       -4.85     2.91e+01
1kr4A             125       -24.45       -4.84     2.91e+01
1jytA             163       -24.44       -4.79     3.06e+01
1jkeA             145       -22.65       -4.74     3.17e+01
8prkA             287       -24.81       -4.73     3.21e+01
1dcpA             104       -22.97       -4.69     3.32e+01
1dcoA             104       -22.97       -4.67     3.38e+01
1amp              291       -24.55       -4.65     3.43e+01
1vid              221       -25.29       -4.65     3.44e+01
1im5A             180       -25.94       -4.64     3.46e+01
1f93A             104       -22.85       -4.60     3.56e+01
1jfgA             374       -26.59       -4.60     3.57e+01
1kaeA             434       -26.67       -4.58     3.64e+01
1jfaA             374       -26.63       -4.55     3.71e+01
1ifc              132       -22.65       -4.49     3.91e+01