meme.adh.oops

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/adh.s
ALPHABET= ACDEFGHIKLMNPQRSTVWY
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
2BHD_STREX               1.0000    255  3BHD_COMTE               1.0000    253  
ADH_DROME                1.0000    255  AP27_MOUSE               1.0000    244  
BA72_EUBSP               1.0000    249  BDH_HUMAN                1.0000    343  
BPHB_PSEPS               1.0000    275  BUDC_KLETE               1.0000    241  
DHES_HUMAN               1.0000    327  DHGB_BACME               1.0000    262  
DHII_HUMAN               1.0000    292  DHMA_FLAS1               1.0000    270  
ENTA_ECOLI               1.0000    248  FIXR_BRAJA               1.0000    278  
GUTD_ECOLI               1.0000    259  HDE_CANTR                1.0000    906  
HDHA_ECOLI               1.0000    255  LIGD_PSEPA               1.0000    305  
NODG_RHIME               1.0000    245  RIDH_KLEAE               1.0000    249  
YINL_LISMO               1.0000    248  YRTP_BACSU               1.0000    238  
CSGA_MYXXA               1.0000    166  DHB2_HUMAN               1.0000    387  
DHB3_HUMAN               1.0000    310  DHCA_HUMAN               1.0000    276  
FABI_ECOLI               1.0000    262  FVT1_HUMAN               1.0000    332  
HMTR_LEIMA               1.0000    287  MAS1_AGRRA               1.0000    476  
PCR_PEA                  1.0000    399  RFBB_NEIGO               1.0000    346  
YURA_MYXXA               1.0000    258  
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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/adh.s -mod oops -protein -nostatus -nmotifs 2 

model:  mod=          oops    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=       33    maxsites=       33    wnsites=       0.8
theta:  prob=            1    spmap=         pam    spfuzz=        120
em:     prior=        dmix    b=               0    maxiter=        50
        distance=    1e-05
data:   n=            9996    N=              33

sample: seed=            0    seqfrac=         1
Dirichlet mixture priors file: prior30.plib
Letter frequencies in dataset:
A 0.111 C 0.012 D 0.050 E 0.055 F 0.036 G 0.090 H 0.018 I 0.057 K 0.052 
L 0.092 M 0.027 N 0.041 P 0.041 Q 0.029 R 0.049 S 0.064 T 0.057 V 0.083 
W 0.010 Y 0.027 
Background letter frequencies (from dataset with add-one prior applied):
A 0.111 C 0.012 D 0.050 E 0.055 F 0.036 G 0.090 H 0.018 I 0.057 K 0.052 
L 0.092 M 0.027 N 0.041 P 0.041 Q 0.029 R 0.049 S 0.064 T 0.057 V 0.083 
W 0.010 Y 0.027 
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MOTIF  1	width =   29   sites =  33   llr = 1118   E-value = 3.6e-165
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--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :162:56112:1:215:::4:::::::11
pos.-specific     C  :1:::::::::::1:::::::::::1:1:
probability       D  ::::::::1:::1::::2:::::::::::
matrix            E  ::::::::1:::21:::5:111:::::::
                  F  :::::31:::2:::::1::::::::::::
                  G  :2:::13::4:::1:1:::11:5:1:11:
                  H  :::::::::1::1:::1::::1:::::::
                  I  :::::::11:::::::::1::::5:2:13
                  K  ::::9:::1:::2:::1::121::1:1::
                  L  :::::::31:6:1:5:215::1:::::12
                  M  ::1::::1:2:1::2:1:1::::::::::
                  N  :::::::::1::::::::::::2:1:41:
                  P  ::::::::::::::::::::3::::::::
                  Q  ::::::::::::1::11:::11:::::::
                  R  ::::::::2:::3::22::21:1:4:1::
                  S  :426::1:11:213:::::1:11:::21:
                  T  :1:2::::1::3:1::::::11::1:11:
                  V  :::::::41::2:1::1:1::::316123
                  W  :::::1:::::::::::::::::::::::
                  Y  9:::::::::::::::::2::2:::::::

         bits    6.7                              
                 6.0                              
                 5.4                              
                 4.7 *                            
Information      4.0 *   *                        
content          3.4 *   *                        
(48.9 bits)      2.7 *  **     *                  
                 2.0 *  ****   *   *  *     * *   
                 1.3 ******** ******* ** * ***** *
                 0.7 *****************************
                 0.0 -----------------------------

Multilevel           YSASKAAVxGLTRSLAxELAPxGIRVNVV
consensus                 FGL  FSE MR D     V    I
sequence                                          
                                                  
                                                  
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	Motif 1 sites sorted by position p-value
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Sequence name             Start   P-value                        Site           
-------------             ----- ---------            -----------------------------
YRTP_BACSU                  155  1.64e-22 GQRGAAVTSA YSASKFAVLGLTESLMQEVRKHNIRVSAL TPSTVASDMS
AP27_MOUSE                  149  6.32e-22 AHVTFPNLIT YSSTKGAMTMLTKAMAMELGPHKIRVNSV NPTVVLTDMG
NODG_RHIME                  152  1.13e-21 GAIGNPGQTN YCASKAGMIGFSKSLAQEIATRNITVNCV APGFIESAMT
BUDC_KLETE                  152  4.04e-21 GHVGNPELAV YSSSKFAVRGLTQTAARDLAPLGITVNGF CPGIVKTPMW
FIXR_BRAJA                  189  6.12e-21 SRVHPFAGSA YATSKAALASLTRELAHDYAPHGIRVNAI APGEIRTDML
DHGB_BACME                  160  7.52e-20 WKIPWPLFVH YAASKGGMKLMTETLALEYAPKGIRVNNI GPGAINTPIN
HMTR_LEIMA                  193  3.35e-19 TNQPLLGYTI YTMAKGALEGLTRSAALELAPLQIRVNGV GPGLSVLVDD
YURA_MYXXA                  160  4.82e-19 AGFRGLPATR YSASKAFLSTFMESLRVDLRGTGVRVTCI YPGFVKSELT
GUTD_ECOLI                  154  4.82e-19 GKVGSKHNSG YSAAKFGGVGLTQSLALDLAEYGITVHSL MLGNLLKSPM
2BHD_STREX                  152  1.11e-18 GLMGLALTSS YGASKWGVRGLSKLAAVELGTDRIRVNSV HPGMTYTPMT
HDHA_ECOLI                  159  1.25e-18 AENKNINMTS YASSKAAASHLVRNMAFDLGEKNIRVNGI APGAILTDAL
DHB2_HUMAN                  232  2.23e-18 GGAPMERLAS YGSSKAAVTMFSSVMRLELSKWGIKVASI QPGGFLTNIA
DHMA_FLAS1                  165  5.53e-18 SFMAEPEAAA YVAAKGGVAMLTRAMAVDLARHGILVNMI APGPVDVTGN
HDE_CANTR                   467  9.65e-18 GIYGNFGQAN YSSSKAGILGLSKTMAIEGAKNNIKVNIV APHAETAMTL
FVT1_HUMAN                  186  2.86e-17 GQLGLFGFTA YSASKFAIRGLAEALQMEVKPYNVYITVA YPPDTDTPGF
BDH_HUMAN                   208  8.20e-17 GRMANPARSP YCITKFGVEAFSDCLRYEMYPLGVKVSVV EPGNFIAATS
RIDH_KLEAE                  160  9.09e-17 GVVPVIWEPV YTASKFAVQAFVHTTRRQVAQYGVRVGAV LPGPVVTALL
DHES_HUMAN                  155  1.37e-16 GLMGLPFNDV YCASKFALEGLCESLAVLLLPFGVHLSLI ECGPVHTAFM
BA72_EUBSP                  157  2.52e-16 GIFGSLSGVG YPASKASVIGLTHGLGREIIRKNIRVVGV APGVVNTDMT
LIGD_PSEPA                  157  1.21e-15 GFMGSALAGP YSAAKAASINLMEGYRQGLEKYGIGVSVC TPANIKSNIA
DHII_HUMAN                  183  1.61e-15 GKVAYPMVAA YSASKFALDGFFSSIRKEYSVSRVNVSIT LCVLGLIDTE
ENTA_ECOLI                  144  1.77e-15 AHTPRIGMSA YGASKAALKSLALSVGLELAGSGVRCNVV SPGSTDTDMQ
3BHD_COMTE                  151  7.81e-15 SWLPIEQYAG YSASKAAVSALTRAAALSCRKQGYAIRVN SIHPDGIYTP
DHB3_HUMAN                  198  8.55e-15 ALFPWPLYSM YSASKAFVCAFSKALQEEYKAKEVIIQVL TPYAVSTAMT
RFBB_NEIGO                  165  1.47e-14 ETTPYAPSSP YSASKAAADHLVRAWQRTYRLPSIVSNCS NNYGPRQFPE
YINL_LISMO                  154  3.24e-14 GLKAYPGGAV YGATKWAVRDLMEVLRMESAQEGTNIRTA TIYPAAINTE