meme.adh.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/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 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=       50    wnsites=       0.8
theta:  prob=            1    spmap=         pam    spfuzz=        120
em:     prior=       megap    b=           49980    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 =   22   sites =  31   llr = 890   E-value = 2.3e-120
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	Motif 1 Description
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Simplified        A  :162:56112:1:215:::4::
pos.-specific     C  :1::::::::::::::::::::
probability       D  ::::::::1::::::::2::::
matrix            E  ::::::::1:::31:::5::11
                  F  :::::31:::3:::::1:::::
                  G  :2:::12::4:::1:1::111:
                  H  :::::::::1::1::::::::1
                  I  :::::::11:::::::::1:::
                  K  ::::a:::1:::2:::1::121
                  L  :::::::31:6:::5:215::1
                  M  ::1::::1:1:1::2:1:1:::
                  N  :::::::::1::::::::::::
                  P  ::::::::::::::::::::4:
                  Q  ::::::::::::1::11:::1:
                  R  ::::::::1:::3::21::21:
                  S  :426::1:11:213:::::1:1
                  T  :1:1::::1::4:2::::::11
                  V  :::::::41::2:1::1:1:::
                  W  :::::1::::::::::::::::
                  Y  a:::::::::::::::::2::2

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

Multilevel           YSASKAAVxGLTRSLAxELAPx
consensus               A FGL  F E MR D    
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  7.98e-19 GQRGAAVTSA YSASKFAVLGLTESLMQEVRKH NIRVSALTPS
FVT1_HUMAN                  186  2.84e-17 GQLGLFGFTA YSASKFAIRGLAEALQMEVKPY NVYITVAYPP
BUDC_KLETE                  152  5.90e-17 GHVGNPELAV YSSSKFAVRGLTQTAARDLAPL GITVNGFCPG
AP27_MOUSE                  149  1.04e-16 AHVTFPNLIT YSSTKGAMTMLTKAMAMELGPH KIRVNSVNPT
NODG_RHIME                  152  4.04e-16 GAIGNPGQTN YCASKAGMIGFSKSLAQEIATR NITVNCVAPG
DHES_HUMAN                  155  1.28e-15 GLMGLPFNDV YCASKFALEGLCESLAVLLLPF GVHLSLIECG
BPHB_PSEPS                  153  2.35e-15 GFYPNGGGPL YTAAKQAIVGLVRELAFELAPY VRVNGVGPGG
GUTD_ECOLI                  154  2.66e-15 GKVGSKHNSG YSAAKFGGVGLTQSLALDLAEY GITVHSLMLG
FIXR_BRAJA                  189  7.64e-15 SRVHPFAGSA YATSKAALASLTRELAHDYAPH GIRVNAIAPG
HMTR_LEIMA                  193  8.56e-15 TNQPLLGYTI YTMAKGALEGLTRSAALELAPL QIRVNGVGPG
DHB2_HUMAN                  232  9.59e-15 GGAPMERLAS YGSSKAAVTMFSSVMRLELSKW GIKVASIQPG
DHGB_BACME                  160  1.68e-14 WKIPWPLFVH YAASKGGMKLMTETLALEYAPK GIRVNNIGPG
3BHD_COMTE                  151  1.68e-14 SWLPIEQYAG YSASKAAVSALTRAAALSCRKQ GYAIRVNSIH
YURA_MYXXA                  160  2.09e-14 AGFRGLPATR YSASKAFLSTFMESLRVDLRGT GVRVTCIYPG
DHB3_HUMAN                  198  3.99e-14 ALFPWPLYSM YSASKAFVCAFSKALQEEYKAK EVIIQVLTPY
YINL_LISMO                  154  4.43e-14 GLKAYPGGAV YGATKWAVRDLMEVLRMESAQE GTNIRTATIY
RIDH_KLEAE                  160  4.92e-14 GVVPVIWEPV YTASKFAVQAFVHTTRRQVAQY GVRVGAVLPG
HDE_CANTR                   467  6.07e-14 GIYGNFGQAN YSSSKAGILGLSKTMAIEGAKN NIKVNIVAPH
DHMA_FLAS1                  165  7.46e-14 SFMAEPEAAA YVAAKGGVAMLTRAMAVDLARH GILVNMIAPG
DHII_HUMAN                  183  9.16e-14 GKVAYPMVAA YSASKFALDGFFSSIRKEYSVS RVNVSITLCV
2BHD_STREX                  152  2.74e-13 GLMGLALTSS YGASKWGVRGLSKLAAVELGTD RIRVNSVHPG
HDHA_ECOLI                  159  4.02e-13 AENKNINMTS YASSKAAASHLVRNMAFDLGEK NIRVNGIAPG
HDE_CANTR                   163  7.77e-13 GLYGNFGQAN YASAKSALLGFAETLAKEGAKY NIKANAIAPL
BDH_HUMAN                   208  9.34e-13 GRMANPARSP YCITKFGVEAFSDCLRYEMYPL GVKVSVVEPG
RFBB_NEIGO                  165  1.02e-12 ETTPYAPSSP YSASKAAADHLVRAWQRTYRLP SIVSNCSNNY
BA72_EUBSP                  157  1.76e-12 GIFGSLSGVG YPASKASVIGLTHGLGREIIRK NIRVVGVAPG
CSGA_MYXXA                   88  1.92e-12 AANTDGGAYA YRMSKAALNMAVRSMSTDLRPE GFVTVLLHPG
LIGD_PSEPA                  157  2.74e-12 GFMGSALAGP YSAAKAASINLMEGYRQGLEKY GIGVSVCTPA
ENTA_ECOLI                  144  1.73e-11 AHTPRIGMSA YGASKAALKSLALSVGLELAGS GVRCNVVSPG
ADH_DROME                   152  7.59e-11 GFNAIYQVPV YSGTKAAVVNFTSSLAKLAPIT GVTAYTVNPG
FABI_ECOLI                  159  8.18e-09 AERAIPNYNV MGLAKASLEANVRYMANAMGPE GVRVNAISAG
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	Motif 1 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
YRTP_BACSU                          8e-19  154_[1]_62
FVT1_HUMAN                        2.8e-17  185_[1]_125
BUDC_KLETE                        5.9e-17  151_[1]_68
AP27_MOUSE                          1e-16  148_[1]_74
NODG_RHIME                          4e-16  151_[1]_72
DHES_HUMAN                        1.3e-15  154_[1]_151
BPHB_PSEPS                        2.4e-15  152_[1]_101
GUTD_ECOLI                        2.7e-15  153_[1]_84
FIXR_BRAJA                        7.6e-15  188_[1]_68
HMTR_LEIMA                        8.6e-15  192_[1]_73
DHB2_HUMAN                        9.6e-15  231_[1]_134
DHGB_BACME                        1.7e-14  159_[1]_81
3BHD_COMTE                        1.7e-14  150_[1]_81
YURA_MYXXA                        2.1e-14  159_[1]_77
DHB3_HUMAN                          4e-14  197_[1]_91
YINL_LISMO                        4.4e-14  153_[1]_73
RIDH_KLEAE                        4.9e-14  159_[1]_68
HDE_CANTR                         7.8e-13  162_[1]_282_[1]_418
DHMA_FLAS1                        7.5e-14  164_[1]_84
DHII_HUMAN                        9.2e-14  182_[1]_88
2BHD_STREX                        2.7e-13  151_[1]_82
HDHA_ECOLI                          4e-13  158_[1]_75
BDH_HUMAN                         9.3e-13  207_[1]_114
RFBB_NEIGO                          1e-12  164_[1]_160
BA72_EUBSP                        1.8e-12  156_[1]_71
CSGA_MYXXA                        1.9e-12  87_[1]_57
LIGD_PSEPA                        2.7e-12  156_[1]_127
ENTA_ECOLI                        1.7e-11  143_[1]_83
ADH_DROME                         7.6e-11  151_[1]_82