From farmer@cse.ucsc.edu  Tue Jul 20 10:41:02 1999
Return-Path: <farmer@cse.ucsc.edu>
Date: Tue, 20 Jul 1999 10:41:00 -0700
From: UCSC Computational Biology <farmer@cse.ucsc.edu>
Subject: UCSC SAM-T98-query results
Apparently-To: karplus@cse.ucsc.edu



The following are search results using the SAM-T98 method
for a sequence query against a database. If there
are no hits associated with this output, then your
score cutoff was too conservative.

Citation:  
  K. Karplus, C. Barrett, and R. Hughey,
  Hidden Markov Models for Detecting Remote Protein Homologies,
  Bioinformatics, to appear, 1998. 
  http://www.cse.ucsc.edu/resesarch/compbio/HMM-apps
--------------------------------------------------------

% Using total residues as number of starting possibilities,
%  0.01 significance at <= ln(0.01)-ln(3791228)= -4.6 - 15.1 = -19.7
% Adjusting for model length gives 3143205 starting points,
%  0.01 significance at <= ln(0.01)-ln(3143205) = -4.6 - 15.0 = -19.6
% If entire sequences are modeled (i.e., no FIMs),
%  0.01 significance at <= ln(0.01)-ln(18113) = -4.6 -  9.8 = -14.4
% Values for 10.0 significance are -12.8, -12.7, and  -7.5.
% Significance level is higher for multiple scoring runs.
% Sequence scores selected if better than:
%	 C1/Simple (-9.000) C2/Complex (-9.000) (select_score=3)
%
% Column 1: NLL-NULL using simple FIM (node 0) insert probabilities
% Column 2: NLL-NULL for the reverse sequence NULL model
% Scores sorted by column 2, best first
%
% Sequence ID   Length      Simple     Reverse      X count
2crd               37       -63.87      -58.05
1big               37       -62.43      -56.07
1lir               37       -60.00      -54.04
2bmt               37       -58.97      -53.30
1mtx               39       -59.25      -53.00
1agt               38       -59.80      -52.98
2ktx               38       -58.06      -52.10
1ktx               38       -58.06      -51.89
1sxm               40       -59.01      -50.96
1bah               37       -56.10      -50.94
1sco               38       -56.75      -49.98
2pta               35       -53.13      -45.97
1bkt               38       -51.95      -45.97
1txm               35       -50.61      -44.11
1tsk               35       -46.29      -40.90
1cmr               31       -43.44      -37.57
1gps               47       -35.72      -29.29
1gpt               47       -35.73      -29.10
1acw               29       -30.97      -24.92
1cn2               67       -26.61      -21.29
1myn               44       -21.53      -13.05
1vna               65       -16.05      -10.33
1vnb               65       -16.05      -10.33
1b3cA              64       -15.99      -10.25
2b3c               64       -15.99      -10.25
2sn3               65       -15.72      -10.17
1chl               36       -16.42       -9.91



; 1 2crd
; 2 2crd
   1 XFTNVSCTTSKECWSVCQRLHNTSRGKCMNKKCRCYS
   2 XFTNVSCTTSKECWSVCQRLHNTSRGKCMNKKCRCYS




; 1 2crd
; 2 1big
   1 XFTNVSCTTSKECWSVCQRLHNTSRGKCMNKKCRCYS
   2 XFTDVKCTGSKQCWPVCKQMFGKPNGKCMNGKCRCYS




; 1 2crd
; 2 1lir
   1 XFTNVSCTTSKECWSVCQRLHNTSRGKCMNKKCRCYS
   2 XFTQESCTASNQCWSICKRLHNTNRGKCMNKKCRCYS




; 1 2crd
; 2 2bmt
   1 XFTNVSCTTSKECWSVCQRLHNTSRGKCMNKKCRCYS
   2 XFTNVSCSASSQCWPVCKKLFGTYRGKCMNSKCRCYS




; 1 2crd
; 2 1mtx
   1 XFTNVSCTTSKECWSVCQRLHNTSRG.KCMNKKCRCYS..
   2 TIINVKCTSPKQCLPPCKAQFGQSAGaKCMNGKCKCYPh.




; 1 2crd
; 2 1agt
   1 .XFTNVSCTTSKECWSVCQRLHNTSRGKCMNKKCRCYS..
   2 gVPINVSCTGSPQCIKPCKDA-GMRFGKCMNRKCHCTPk.




; 1 2crd
; 2 2ktx
   1 .XFTNVSCTTSKECWSVCQRLHNTSRGKCMNKKCRCYS..
   2 gVEINVKCSGSPQCLKPCKDA-GMRFGKCMNRKCHCTPk.




; 1 2crd
; 2 1ktx
   1 .XFTNVSCTTSKECWSVCQRLHNTSRGKCMNKKCRCYS..
   2 gVEINVKCSGSPQCLKPCKDA-GMRFGKCMNRKCHCTPx.




; 1 2crd
; 2 1sxm
   1 XFTNVSCTTSKECWSVCQRLHNTSRG.KCMNKKCRCYS...
   2 TIINVKCTSPKQCSKPCKELYGSSAGaKCMNGKCKCYNnx.




; 1 2crd
; 2 1bah
   1 XFTNVSCTTSKECWSVCQRLHNTSRGKCMNKKCRCYS
   2 XFTNVSCTTSKEXWSVCQRLHNTSRGKCMNKKXRCYS