meme.farntrans5.tcm

EM算法的改进

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MEME - Motif discovery tool
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MEME version 3.5.3 (Release date: 2006-03-08 09:30:25 +1000 (Wed, 08 Mar 2006))

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme.nbcr.net.
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REFERENCE
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If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to discover
motifs in biopolymers", Proceedings of the Second International
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
AAAI Press, Menlo Park, California, 1994.
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TRAINING SET
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DATAFILE= /home/tbailey/tests/farntrans5.s
ALPHABET= ACDEFGHIKLMNPQRSTVWY
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
RAM1_YEAST               1.0000    431  PFTB_RAT                 1.0000    437  
BET2_YEAST               1.0000    325  RATRABGERB               1.0000    331  
CAL1_YEAST               1.0000    376  
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COMMAND LINE SUMMARY
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This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme /home/tbailey/tests/farntrans5.s -mod tcm -protein -nostatus -nmotifs 2 

model:  mod=           tcm    nmotifs=         2    evt=           inf
object function=  E-value of product of p-values
width:  minw=            8    maxw=           50    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        2    maxsites=       25    wnsites=       0.8
theta:  prob=            1    spmap=         pam    spfuzz=        120
em:     prior=       megap    b=            9500    maxiter=        50
        distance=    1e-05
data:   n=            1900    N=               5

sample: seed=            0    seqfrac=         1
Dirichlet mixture priors file: prior30.plib
Letter frequencies in dataset:
A 0.061 C 0.037 D 0.062 E 0.061 F 0.044 G 0.075 H 0.030 I 0.053 K 0.051 
L 0.114 M 0.021 N 0.034 P 0.041 Q 0.038 R 0.041 S 0.078 T 0.046 V 0.057 
W 0.018 Y 0.041 
Background letter frequencies (from dataset with add-one prior applied):
A 0.061 C 0.037 D 0.061 E 0.060 F 0.044 G 0.075 H 0.030 I 0.053 K 0.051 
L 0.113 M 0.021 N 0.034 P 0.041 Q 0.039 R 0.041 S 0.078 T 0.046 V 0.057 
W 0.018 Y 0.041 
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MOTIF  1	width =   30   sites =  24   llr = 854   E-value = 2.2e-094
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	Motif 1 Description
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Simplified        A  :::2::::1:2:11:1:1413314:1:1::
pos.-specific     C  ::::1::::::::2::132::::1::::::
probability       D  ::::21::11:6::::::::::::::2:13
matrix            E  ::::::1114::::::::::::::::1111
                  F  :16:::::::::111:31::::::::::1:
                  G  861241:42:::221:::2:22::::3::1
                  H  ::::::::11:4::2::::::::::::::1
                  I  ::1:::1::::::::1:::1:1::42:11:
                  K  :::::1::3::::::::::::::::::2::
                  L  ::21:::::2::31::1::5::9:55::4:
                  M  ::::::::::::::::::::::::::::::
                  N  :1:1:::21:::::::::::1:::::1:::
                  P  ::::::5:::2:::::::::::::::::::
                  Q  :::1::::1:::::1:::::1:::::::::
                  R  :::::3:::::::2:::::::::::::1::
                  S  :1:2::::::2:::13:1::32:3::12::
                  T  ::::::::::::2::5:1:1:1:1:1:::1
                  V  :::::::1::3:2:::::12::::1:::::
                  W  ::::::::::::::::13::::::::::::
                  Y  :::::::::::::14:31:::::::1::::

         bits    5.8                               
                 5.2                               
                 4.6                               
                 4.0                               
Information      3.5            *                  
content          2.9 *          *          *       
(51.4 bits)      2.3 ***        *   * **   * *     
                 1.7 ***   ** ***  ***** * ****    
                 1.2 ******************************
                 0.6 ******************************
                 0.0 ------------------------------

Multilevel           GGFGGRPGKEVDLCYTFCALAALALLGSLD
consensus                     LAH  HSYWCVSS SI     
sequence                       P       G           
                                                   
                                                   
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	Motif 1 sites sorted by position p-value
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Sequence name             Start   P-value                         Site           
-------------             ----- ---------            ------------------------------
BET2_YEAST                  223  7.28e-22 WWLCERQLPE GGLNGRPSKLPDVCYSWWVLSSLAIIGRLD WINYEKLTEF
RATRABGERB                  227  6.18e-21 WWLCERQLPS GGLNGRPEKLPDVCYSWWVLASLKIIGRLH WIDREKLRSF
CAL1_YEAST                  275  9.17e-20 LNASYDQSDD GGFQGRENKFADTCYAFWCLNSLHLLTKDW KMLCQTELVT
PFTB_RAT                    237  1.15e-19 EWIARCQNWE GGIGGVPGMEAHGGYTFCGLAALVILKKER SLNLKSLLQW
PFTB_RAT                    138  4.30e-19 QFLELCQSPD GGFGGGPGQYPHLAPTYAAVNALCIIGTEE AYNVINREKL
RATRABGERB                  179  7.36e-19 EFVLSCMNFD GGFGCRPGSESHAGQIYCCTGFLAITSQLH QVNSDLLGWW
RATRABGERB                  131  8.19e-19 AYVQSLQKED GSFAGDIWGEIDTRFSFCAVATLALLGKLD AINVEKAIEF
BET2_YEAST                  172  2.10e-18 DFVLKCYNFD GGFGLCPNAESHAAQAFTCLGALAIANKLD MLSDDQLEEI
RATRABGERB                  276  1.43e-17 FILACQDEET GGFADRPGDMVDPFHTLFGIAGLSLLGEEQ IKPVSPVFCM
BET2_YEAST                  124  3.41e-17 SFIRGNQLED GSFQGDRFGEVDTRFVYTALSALSILGELT SEVVDPAVDF
RAM1_YEAST                  247  5.00e-17 YLKNCQNYEG GFGSCPHVDEAHGGYTFCATASLAILRSMD QINVEKLLEW
BET2_YEAST                  272  6.64e-17 FILKCQDEKK GGISDRPENEVDVFHTVFGVAGLSLMGYDN LVPIDPIYCM
RAM1_YEAST                  145  1.27e-16 VKLFTISPSG GPFGGGPGQLSHLASTYAAINALSLCDNID GCWDRIDRKG
PFTB_RAT                    286  3.17e-16 WVTSRQMRFE GGFQGRCNKLVDGCYSFWQAGLLPLLHRAL HAQGDPALSM
RAM1_YEAST                  296  3.47e-16 WSSARQLQEE RGFCGRSNKLVDGCYSFWVGGSAAILEAFG YGQCFNKHAL
PFTB_RAT                    348  4.30e-15 YILMCCQCPA GGLLDKPGKSRDFYHTCYCLSGLSIAQHFG SGAMLHDVVM
RATRABGERB                   83  2.40e-14 VFIKSCQHEC GGVSASIGHDPHLLYTLSAVQILTLYDSIH VINVDKVVAY
PFTB_RAT                    189  2.81e-14 QYLYSLKQPD GSFLMHVGGEVDVRSAYCAASVASLTNIIT PDLFEGTAEW
BET2_YEAST                   73  7.78e-14 FVLSCWDDKY GAFAPFPRHDAHLLTTLSAVQILATYDALD VLGKDRKVRL
CAL1_YEAST                  205  1.14e-13 LLGYIMSQQC YNGAFGAHNEPHSGYTSCALSTLALLSSLE KLSDKFKEDT
RAM1_YEAST                  198  1.33e-13 WLISLKEPNG GFKTCLEVGEVDTRGIYCALSIATLLNILT EELTEGVLNY
RAM1_YEAST                  349  3.52e-13 ILYCCQEKEQ PGLRDKPGAHSDFYHTNYCLLGLAVAESSY SCTPNDSPHN
CAL1_YEAST                  327  5.47e-13 LLDRTQKTLT GGFSKNDEEDADLYHSCLGSAALALIEGKF NGELCIPQEI
BET2_YEAST                   24  3.11e-10 RYIESLDTNK HNFEYWLTEHLRLNGIYWGLTALCVLDSPE TFVKEEVISF
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	Motif 1 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
BET2_YEAST                        3.1e-10  23_[1]_19_[1]_21_[1]_18_[1]_21_
                                           [1]_19_[1]_24
RATRABGERB                        2.4e-14  82_[1]_18_[1]_18_[1]_18_[1]_19_[1]_26
CAL1_YEAST                        1.1e-13  204_[1]_40_[1]_22_[1]_20
PFTB_RAT                          4.3e-15  137_[1]_21_[1]_18_[1]_19_[1]_32_
                                           [1]_60
RAM1_YEAST                        1.3e-13  144_[1]_23_[1]_19_[1]_19_[1]_23_