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  • Committer: Package Import Robot
  • Author(s): Charles Plessy
  • Date: 2013-09-22 13:39:48 UTC
  • mfrom: (3.1.11 sid)
  • Revision ID: package-import@ubuntu.com-20130922133948-c6z62zegjyp7ztou
Tags: 1.6.922-1
http://bugs.debian.org/722910
* New upstream release.
* Replaces and Breaks grinder (<< 0.5.3-3~) because of overlaping contents.
  Closes: #722910
* Stop Replacing and Breaking bioperl ( << 1.6.9 ): not needed anymore. 

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t/data/test-3.0-2.meme
 
1
********************************************************************************
 
2
MEME - Motif discovery tool
 
3
********************************************************************************
 
4
MEME version 3.0 (Release date: 2002/04/02 00:11:59)
 
5
 
 
6
For further information on how to interpret these results or to get
 
7
a copy of the MEME software please access http://meme.sdsc.edu.
 
8
 
 
9
This file may be used as input to the MAST algorithm for searching
 
10
sequence databases for matches to groups of motifs.  MAST is available
 
11
for interactive use and downloading at http://meme.sdsc.edu.
 
12
********************************************************************************
 
13
 
 
14
 
 
15
********************************************************************************
 
16
REFERENCE
 
17
********************************************************************************
 
18
If you use this program in your research, please cite:
 
19
 
 
20
Timothy L. Bailey and Charles Elkan,
 
21
"Fitting a mixture model by expectation maximization to discover
 
22
motifs in biopolymers", Proceedings of the Second International
 
23
Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
 
24
AAAI Press, Menlo Park, California, 1994.
 
25
********************************************************************************
 
26
 
 
27
 
 
28
********************************************************************************
 
29
TRAINING SET
 
30
********************************************************************************
 
31
DATAFILE= test.fasta
 
32
ALPHABET= ACGT
 
33
Sequence name            Weight Length  Sequence name            Weight Length  
 
34
-------------            ------ ------  -------------            ------ ------  
 
35
68723                    1.0000   2000  16939                    1.0000   2001  
 
36
20754                    1.0000   2001  6707                     1.0000   2000  
 
37
20755                    1.0000   2000  6700                     1.0000   2002  
 
38
20760                    1.0000   2000  20761                    1.0000   2000  
 
39
20762                    1.0000   2000  
 
40
********************************************************************************
 
41
 
 
42
********************************************************************************
 
43
COMMAND LINE SUMMARY
 
44
********************************************************************************
 
45
This information can also be useful in the event you wish to report a
 
46
problem with the MEME software.
 
47
 
 
48
command: meme test.fasta -dna -nostatus -nmotifs 2 -minsites 8 -maxw 20 -revcomp 
 
49
 
 
50
model:  mod=         zoops    nmotifs=         2    evt=           inf
 
51
object function=  E-value of product of p-values
 
52
width:  minw=            8    maxw=           20    minic=        0.00
 
53
width:  wg=             11    ws=              1    endgaps=       yes
 
54
nsites: minsites=        8    maxsites=        9    wnsites=       0.8
 
55
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
 
56
em:     prior=   dirichlet    b=            0.01    maxiter=        50
 
57
        distance=    1e-05
 
58
data:   n=           18004    N=               9
 
59
strands: + -
 
60
sample: seed=            0    seqfrac=         1
 
61
Letter frequencies in dataset:
 
62
A 0.295 C 0.205 G 0.205 T 0.295 
 
63
Background letter frequencies (from dataset with add-one prior applied):
 
64
A 0.295 C 0.205 G 0.205 T 0.295 
 
65
********************************************************************************
 
66
 
 
67
 
 
68
********************************************************************************
 
69
MOTIF  1        width =   20   sites =   8   llr = 147   E-value = 1.3e-002
 
70
********************************************************************************
 
71
--------------------------------------------------------------------------------
 
72
        Motif 1 Description
 
73
--------------------------------------------------------------------------------
 
74
Simplified        A  ::a1::931:6:348:1::1
 
75
pos.-specific     C  aa:::8:11841:331:139
 
76
probability       G  :::9::::63::84::3:8:
 
77
matrix            T  ::::a3161::9:::969::
 
78
 
 
79
         bits    2.3 **                  
 
80
                 2.1 **                  
 
81
                 1.8 *** *               
 
82
                 1.6 *****              *
 
83
Information      1.4 ******   * **  * ***
 
84
content          1.1 *******  * ** ** ***
 
85
(26.5 bits)      0.9 *******  **** ** ***
 
86
                 0.7 ******* ***** ******
 
87
                 0.5 ********************
 
88
                 0.2 ********************
 
89
                 0.0 --------------------
 
90
 
 
91
Multilevel           CCAGTCATGCATGAATTTGC
 
92
consensus                 T A GC AGC G C 
 
93
sequence                          C      
 
94
                                         
 
95
--------------------------------------------------------------------------------
 
96
 
 
97
--------------------------------------------------------------------------------
 
98
        Motif 1 sites sorted by position p-value
 
99
--------------------------------------------------------------------------------
 
100
Sequence name            Strand  Start   P-value                    Site      
 
101
-------------            ------  ----- ---------            --------------------
 
102
20761                        +   1879  6.50e-13 TCTGATTAAG CCAGTCATGCATGGATTTGC ATTTTGGTTG
 
103
20760                        +   1875  6.50e-13 CCCAGTCACG CCAGTCATGCATGGATTTGC ATTTTGATTG
 
104
6700                         +   1100  2.27e-10 CCTGCTCATG CCAGTCATGGATAAATTTGC ATCTGGCTTA
 
105
20755                        +   1478  5.08e-10 CCCTGTCAGG CCAGTTATGGATGAATGTGC ACTTAANNNN
 
106
6707                         +   1431  6.11e-09 TCACACAGAT CCAGTCAATCCTGCCTGTCC ATCTCAATGA
 
107
20762                        +   1878  1.89e-08 CCTGGTTAGG CCAGTTAAACACAGATTTGC ATTTTGGTTA
 
108
16939                        -    914  2.01e-08 ACTTTTCCTT CCAATCATGCCTGCCCTTGA ACCCTATTGG
 
109
20754                        +   1175  6.73e-08 GCTCACCTTG CCAGTCTCCCCTGAATACCC TACATGCCCT
 
110
--------------------------------------------------------------------------------
 
111
 
 
112
--------------------------------------------------------------------------------
 
113
        Motif 1 block diagrams
 
114
--------------------------------------------------------------------------------
 
115
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 
116
-------------            ----------------  -------------
 
117
20761                             6.5e-13  1878_[+1]_102
 
118
20760                             6.5e-13  1874_[+1]_106
 
119
6700                              2.3e-10  1099_[+1]_883
 
120
20755                             5.1e-10  1477_[+1]_503
 
121
6707                              6.1e-09  1430_[+1]_550
 
122
20762                             1.9e-08  1877_[+1]_103
 
123
16939                               2e-08  913_[-1]_1068
 
124
20754                             6.7e-08  1174_[+1]_807
 
125
--------------------------------------------------------------------------------
 
126
 
 
127
--------------------------------------------------------------------------------
 
128
        Motif 1 in BLOCKS format
 
129
--------------------------------------------------------------------------------
 
130
BL   MOTIF 1 width=20 seqs=8
 
131
20761                    ( 1879) CCAGTCATGCATGGATTTGC  1 
 
132
20760                    ( 1875) CCAGTCATGCATGGATTTGC  1 
 
133
6700                     ( 1100) CCAGTCATGGATAAATTTGC  1 
 
134
20755                    ( 1478) CCAGTTATGGATGAATGTGC  1 
 
135
6707                     ( 1431) CCAGTCAATCCTGCCTGTCC  1 
 
136
20762                    ( 1878) CCAGTTAAACACAGATTTGC  1 
 
137
16939                    (  914) CCAATCATGCCTGCCCTTGA  1 
 
138
20754                    ( 1175) CCAGTCTCCCCTGAATACCC  1 
 
139
//
 
140
 
 
141
--------------------------------------------------------------------------------
 
142
 
 
143
--------------------------------------------------------------------------------
 
144
        Motif 1 position-specific scoring matrix
 
145
--------------------------------------------------------------------------------
 
146
log-odds matrix: alength= 4 w= 20 n= 17833 bayes= 11.1216 E= 1.3e-002 
 
147
  -965    229   -965   -965 
 
148
  -965    229   -965   -965 
 
149
   176   -965   -965   -965 
 
150
  -124   -965    210   -965 
 
151
  -965   -965   -965    176 
 
152
  -965    187   -965    -24 
 
153
   157   -965   -965   -124 
 
154
   -24    -71   -965    108 
 
155
  -124    -71    161   -124 
 
156
  -965    187     29   -965 
 
157
   108     87   -965   -965 
 
158
  -965    -71   -965    157 
 
159
   -24   -965    187   -965 
 
160
    34     29     87   -965 
 
161
   134     29   -965   -965 
 
162
  -965    -71   -965    157 
 
163
  -124   -965     29    108 
 
164
  -965    -71   -965    157 
 
165
  -965     29    187   -965 
 
166
  -124    210   -965   -965 
 
167
--------------------------------------------------------------------------------
 
168
 
 
169
--------------------------------------------------------------------------------
 
170
        Motif 1 position-specific probability matrix
 
171
--------------------------------------------------------------------------------
 
172
letter-probability matrix: alength= 4 w= 20 n= 17833 E= 1.3e-002 
 
173
 0.000369  0.999007  0.000255  0.000369 
 
174
 0.000369  0.999007  0.000255  0.000369 
 
175
 0.999120  0.000255  0.000255  0.000369 
 
176
 0.125213  0.000255  0.874163  0.000369 
 
177
 0.000369  0.000255  0.000255  0.999120 
 
178
 0.000369  0.749319  0.000255  0.250057 
 
179
 0.874276  0.000255  0.000255  0.125213 
 
180
 0.250057  0.125099  0.000255  0.624589 
 
181
 0.125213  0.125099  0.624475  0.125213 
 
182
 0.000369  0.749319  0.249943  0.000369 
 
183
 0.624589  0.374787  0.000255  0.000369 
 
184
 0.000369  0.125099  0.000255  0.874276 
 
185
 0.250057  0.000255  0.749319  0.000369 
 
186
 0.374901  0.249943  0.374787  0.000369 
 
187
 0.749432  0.249943  0.000255  0.000369 
 
188
 0.000369  0.125099  0.000255  0.874276 
 
189
 0.125213  0.000255  0.249943  0.624589 
 
190
 0.000369  0.125099  0.000255  0.874276 
 
191
 0.000369  0.249943  0.749319  0.000369 
 
192
 0.125213  0.874163  0.000255  0.000369 
 
193
--------------------------------------------------------------------------------
 
194
 
 
195
 
 
196
 
 
197
 
 
198
 
 
199
Time 75.70 secs.
 
200
 
 
201
********************************************************************************
 
202
 
 
203
 
 
204
********************************************************************************
 
205
MOTIF  2        width =   15   sites =   8   llr = 117   E-value = 1.2e+003
 
206
********************************************************************************
 
207
--------------------------------------------------------------------------------
 
208
        Motif 2 Description
 
209
--------------------------------------------------------------------------------
 
210
Simplified        A  :1a39:::::18:::
 
211
pos.-specific     C  ::::1:::8a:::::
 
212
probability       G  96:3::1:::::4::
 
213
matrix            T  13:5:a9a3:936aa
 
214
 
 
215
         bits    2.3          *     
 
216
                 2.1          *     
 
217
                 1.8   *  * * *   **
 
218
                 1.6 * *  * * *   **
 
219
Information      1.4 * * ******   **
 
220
content          1.1 * * *******  **
 
221
(21.0 bits)      0.9 * * ***********
 
222
                 0.7 *** ***********
 
223
                 0.5 ***************
 
224
                 0.2 ***************
 
225
                 0.0 ---------------
 
226
 
 
227
Multilevel           GGATATTTCCTATTT
 
228
consensus             T A    T  TG  
 
229
sequence                G           
 
230
                                    
 
231
--------------------------------------------------------------------------------
 
232
 
 
233
--------------------------------------------------------------------------------
 
234
        Motif 2 sites sorted by position p-value
 
235
--------------------------------------------------------------------------------
 
236
Sequence name            Strand  Start   P-value                 Site    
 
237
-------------            ------  ----- ---------            ---------------
 
238
20762                        +   1845  2.62e-09 TCCAGGAACA GGATATTTCCTATTT TTGAGAGTCC
 
239
6700                         +   1068  2.62e-09 TTTCAGAACA GGATATTTCCTATTT TGAGTATCCT
 
240
20755                        +   1445  2.84e-08 GCCAAGGGTG GGATATTTTCTATTT TGTAGAGTCC
 
241
20754                        -    664  5.62e-08 TTTCTTAGAA GGAAATTTCCTTGTT CTCTTTCTAT
 
242
20761                        +    670  1.06e-07 GAAGAAAAAG GAAGATTTCCTAGTT AACAATTCAA
 
243
68723                        -   1925  5.26e-07 TTGCTTTCTT TGAGATGTCCTAGTT CACTCCTAAA
 
244
20760                        -    651  5.56e-07 TTTAAACTTG GTAAATTTTCTTTTT CTTCACATTT
 
245
16939                        -   1616  6.78e-07 TAGTTCAGTT GTATCTTTCCAATTT TGATGTTTGG
 
246
--------------------------------------------------------------------------------
 
247
 
 
248
--------------------------------------------------------------------------------
 
249
        Motif 2 block diagrams
 
250
--------------------------------------------------------------------------------
 
251
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 
252
-------------            ----------------  -------------
 
253
20762                             2.6e-09  1844_[+2]_141
 
254
6700                              2.6e-09  1067_[+2]_920
 
255
20755                             2.8e-08  1444_[+2]_541
 
256
20754                             5.6e-08  663_[-2]_1323
 
257
20761                             1.1e-07  669_[+2]_1316
 
258
68723                             5.3e-07  1924_[-2]_61
 
259
20760                             5.6e-07  650_[-2]_1335
 
260
16939                             6.8e-07  1615_[-2]_371
 
261
--------------------------------------------------------------------------------
 
262
 
 
263
--------------------------------------------------------------------------------
 
264
        Motif 2 in BLOCKS format
 
265
--------------------------------------------------------------------------------
 
266
BL   MOTIF 2 width=15 seqs=8
 
267
20762                    ( 1845) GGATATTTCCTATTT  1 
 
268
6700                     ( 1068) GGATATTTCCTATTT  1 
 
269
20755                    ( 1445) GGATATTTTCTATTT  1 
 
270
20754                    (  664) GGAAATTTCCTTGTT  1 
 
271
20761                    (  670) GAAGATTTCCTAGTT  1 
 
272
68723                    ( 1925) TGAGATGTCCTAGTT  1 
 
273
20760                    (  651) GTAAATTTTCTTTTT  1 
 
274
16939                    ( 1616) GTATCTTTCCAATTT  1 
 
275
//
 
276
 
 
277
--------------------------------------------------------------------------------
 
278
 
 
279
--------------------------------------------------------------------------------
 
280
        Motif 2 position-specific scoring matrix
 
281
--------------------------------------------------------------------------------
 
282
log-odds matrix: alength= 4 w= 15 n= 17878 bayes= 11.1253 E= 1.2e+003 
 
283
  -965   -965    210   -124 
 
284
  -124   -965    161    -24 
 
285
   176   -965   -965   -965 
 
286
   -24   -965     29     76 
 
287
   157    -71   -965   -965 
 
288
  -965   -965   -965    176 
 
289
  -965   -965    -71    157 
 
290
  -965   -965   -965    176 
 
291
  -965    187   -965    -24 
 
292
  -965    229   -965   -965 
 
293
  -124   -965   -965    157 
 
294
   134   -965   -965    -24 
 
295
  -965   -965     87    108 
 
296
  -965   -965   -965    176 
 
297
  -965   -965   -965    176 
 
298
--------------------------------------------------------------------------------
 
299
 
 
300
--------------------------------------------------------------------------------
 
301
        Motif 2 position-specific probability matrix
 
302
--------------------------------------------------------------------------------
 
303
letter-probability matrix: alength= 4 w= 15 n= 17878 E= 1.2e+003 
 
304
 0.000369  0.000255  0.874163  0.125213 
 
305
 0.125213  0.000255  0.624475  0.250057 
 
306
 0.999120  0.000255  0.000255  0.000369 
 
307
 0.250057  0.000255  0.249943  0.499745 
 
308
 0.874276  0.125099  0.000255  0.000369 
 
309
 0.000369  0.000255  0.000255  0.999120 
 
310
 0.000369  0.000255  0.125099  0.874276 
 
311
 0.000369  0.000255  0.000255  0.999120 
 
312
 0.000369  0.749319  0.000255  0.250057 
 
313
 0.000369  0.999007  0.000255  0.000369 
 
314
 0.125213  0.000255  0.000255  0.874276 
 
315
 0.749432  0.000255  0.000255  0.250057 
 
316
 0.000369  0.000255  0.374787  0.624589 
 
317
 0.000369  0.000255  0.000255  0.999120 
 
318
 0.000369  0.000255  0.000255  0.999120 
 
319
--------------------------------------------------------------------------------
 
320
 
 
321
 
 
322
 
 
323
 
 
324
 
 
325
Time 152.20 secs.
 
326
 
 
327
********************************************************************************
 
328
 
 
329
 
 
330
********************************************************************************
 
331
SUMMARY OF MOTIFS
 
332
********************************************************************************
 
333
 
 
334
--------------------------------------------------------------------------------
 
335
        Combined block diagrams: non-overlapping sites with p-value < 0.0001
 
336
--------------------------------------------------------------------------------
 
337
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 
338
-------------            ----------------  -------------
 
339
68723                            2.83e-04  473_[-1(8.43e-06)]_[+1(1.38e-05)]_[+1(1.38e-05)]_35_[-1(3.15e-06)]_[+1(1.38e-05)]_9_[-1(7.89e-05)]_63_[-1(2.97e-06)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_26_[+2(4.37e-06)]_46_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_6_[-1(7.97e-06)]_24_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_1_[-2(5.92e-05)]_279_[-1(8.43e-06)]_[+1(1.38e-05)]_[+2(5.60e-05)]_157_[-2(5.26e-07)]_61
 
340
16939                            3.50e-06  913_[-1(2.01e-08)]_682_[-2(6.78e-07)]_205_[+1(5.80e-05)]_146
 
341
20754                            1.05e-06  39_[-2(1.78e-05)]_4_[+1(4.78e-06)]_564_[-2(7.42e-05)]_6_[-2(5.62e-08)]_146_[+2(3.98e-05)]_335_[+1(6.73e-08)]_93_[+1(5.54e-05)]_694
 
342
6707                             2.26e-05  173_[+1(4.46e-05)]_655_[-2(5.60e-05)]_3_[+1(3.06e-06)]_12_[+1(4.78e-06)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.93e-05)]_181_[-1(3.26e-05)]_251_[+1(6.11e-09)]_329_[+1(6.34e-05)]_201
 
343
20755                            5.26e-09  160_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_3_[+1(6.41e-06)]_219_[-1(4.80e-05)]_962_[+2(2.84e-08)]_18_[+1(5.08e-10)]_6_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_14_[+1(7.97e-06)]_83
 
344
6700                             2.48e-10  48_[+1(7.97e-06)]_267_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_129_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_3_[+1(4.41e-06)]_280_[+2(2.62e-09)]_17_[+1(2.27e-10)]_101_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+2(7.29e-05)]_[+1(6.41e-06)]_604_[-1(8.43e-06)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_3
 
345
20760                            1.53e-10  259_[-1(6.20e-05)]_339_[-2(3.17e-05)]_17_[-2(5.56e-07)]_436_[-2(4.06e-05)]_7_[+1(2.95e-07)]_6_[-1(1.12e-05)]_705_[+1(6.50e-13)]_106
 
346
20761                            3.10e-11  397_[-2(1.10e-06)]_257_[+2(1.06e-07)]_382_[-2(5.60e-05)]_[+2(7.29e-05)]_[-1(3.24e-06)]_[+1(1.38e-05)]_[+1(1.38e-05)]_722_[+1(6.50e-13)]_102
 
347
20762                            1.72e-08  134_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_92_[+2(9.22e-05)]_517_[+1(7.97e-06)]_7_[-1(4.78e-06)]_439_[+2(2.62e-09)]_18_[+1(1.89e-08)]_103
 
348
--------------------------------------------------------------------------------
 
349
 
 
350
********************************************************************************
 
351
 
 
352
 
 
353
********************************************************************************
 
354
Stopped because nmotifs = 2 reached.
 
355
********************************************************************************
 
356
 
 
357
CPU: crick
 
358
 
 
359
********************************************************************************