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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
| author | iuc |
|---|---|
| date | Thu, 17 May 2018 14:11:27 -0400 |
| parents | |
| children | 3e5c80594237 |
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******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.12.0 (Release date: Tue Jun 27 16:22:50 2017 -0700) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme-suite.org . 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-suite.org . ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** 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. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= meme_input_1.fasta ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr21_19617074_19617124_ 1.0000 50 chr21_26934381_26934431_ 1.0000 50 chr21_28217753_28217803_ 1.0000 50 chr21_31710037_31710087_ 1.0000 50 chr21_31744582_31744632_ 1.0000 50 chr21_31768316_31768366_ 1.0000 50 chr21_31914206_31914256_ 1.0000 50 chr21_31933633_31933683_ 1.0000 50 chr21_31962741_31962791_ 1.0000 50 chr21_31964683_31964733_ 1.0000 50 chr21_31973364_31973414_ 1.0000 50 chr21_31992870_31992920_ 1.0000 50 chr21_32185595_32185645_ 1.0000 50 chr21_32202076_32202126_ 1.0000 50 chr21_32253899_32253949_ 1.0000 50 chr21_32410820_32410870_ 1.0000 50 chr21_36411748_36411798_ 1.0000 50 chr21_37838750_37838800_ 1.0000 50 chr21_45705687_45705737_ 1.0000 50 chr21_45971413_45971463_ 1.0000 50 chr21_45978668_45978718_ 1.0000 50 chr21_45993530_45993580_ 1.0000 50 chr21_46020421_46020471_ 1.0000 50 chr21_46031920_46031970_ 1.0000 50 chr21_46046964_46047014_ 1.0000 50 chr21_46057197_46057247_ 1.0000 50 chr21_46086869_46086919_ 1.0000 50 chr21_46102103_46102153_ 1.0000 50 chr21_47517957_47518007_ 1.0000 50 chr21_47575506_47575556_ 1.0000 50 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme meme_input_1.fasta -o meme_test1_out -nostatus -maxsize 1000000 model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 50 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 30 wnsites= 0.8 theta: spmap= pam spfuzz= 120 global: substring= yes branching= no wbranch= no em: prior= megap b= 7500 maxiter= 50 distance= 1e-05 data: n= 1500 N= 30 shuffle= -1 sample: seed= 0 ctfrac= -1 maxwords= -1 Dirichlet mixture priors file: prior30.plib Letter frequencies in dataset: A 0.294 C 0.231 D 0.000 E 0.000 F 0.000 G 0.257 H 0.000 I 0.000 K 0.000 L 0.000 M 0.000 N 0.000 P 0.000 Q 0.000 R 0.000 S 0.000 T 0.217 V 0.000 W 0.000 Y 0.000 Background letter frequencies (from dataset with add-one prior applied): A 0.291 C 0.229 D 0.001 E 0.001 F 0.001 G 0.255 H 0.001 I 0.001 K 0.001 L 0.001 M 0.001 N 0.001 P 0.001 Q 0.001 R 0.001 S 0.001 T 0.215 V 0.001 W 0.001 Y 0.001 ******************************************************************************** ******************************************************************************** MOTIF GGGGTATAAAA MEME-1 width = 11 sites = 25 llr = 239 E-value = 2.4e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2323:a:a8a8 pos.-specific C ::3:::::::: probability D ::::::::::: matrix E ::::::::::: F ::::::::::: G 7746::::::1 H ::::::::::: I ::::::::::: K ::::::::::: L ::::::::::: M ::::::::::: N ::::::::::: P ::::::::::: Q ::::::::::: R ::::::::::: S ::::::::::: T 1:2:a:a:2:: V ::::::::::: W ::::::::::: Y ::::::::::: bits 10.6 9.5 8.5 7.4 Relative 6.3 Entropy 5.3 (13.8 bits) 4.2 3.2 2.1 * ** 1.1 ** ******** 0.0 ----------- Multilevel GGGGTATAAAA consensus AACA T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------- chr21_46046964_46047014_ 13 1.06e-06 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC chr21_46057197_46057247_ 37 3.41e-06 ACAGGCCCTG GGCATATAAAA GCC chr21_45971413_45971463_ 10 3.41e-06 CAGGCCCTG GGCATATAAAA GCCCCAGCAG chr21_31964683_31964733_ 14 3.41e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC chr21_45993530_45993580_ 8 4.00e-06 CCAAGGA GGAGTATAAAA GCCCCACAAA chr21_32202076_32202126_ 14 5.01e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC chr21_46031920_46031970_ 16 6.06e-06 ATACCCAGGG AGGGTATAAAA CCTCAGCAGC chr21_32410820_32410870_ 22 8.67e-06 AATCACTGAG GATGTATAAAA GTCCCAGGGA chr21_32185595_32185645_ 19 8.67e-06 CACCAGAGCT GGGATATATAA AGAAGGTTCT chr21_31992870_31992920_ 17 8.67e-06 CACTATTGAA GATGTATAAAA TTTCATTTGC chr21_46020421_46020471_ 3 1.21e-05 GA GACATATAAAA GCCAACATCC chr21_47517957_47518007_ 33 1.59e-05 CCGGCGGGGC GGGGTATAAAG GGGGCGG chr21_45978668_45978718_ 5 1.59e-05 CAGA GGGGTATAAAG GTTCCGACCA chr21_31914206_31914256_ 16 1.68e-05 CCCACTACTT AGAGTATAAAA TCATTCTGAG chr21_32253899_32253949_ 20 2.03e-05 CACCAGCAAG GATATATAAAA GCTCAGGAGT chr21_31744582_31744632_ 13 3.06e-05 CAGGTCTAAG AGCATATATAA CTTGGAGTCC chr21_19617074_19617124_ 40 3.06e-05 CCTCGGGACG TGGGTATATAA chr21_45705687_45705737_ 38 3.82e-05 CGTGGTCGCG GGGGTATAACA GC chr21_31768316_31768366_ 1 3.82e-05 . AACGTATATAA ATGGTCCTGT chr21_47575506_47575556_ 31 4.02e-05 GCTGCCGGTG AGCGTATAAAG GCCCTGGCG chr21_26934381_26934431_ 28 5.52e-05 AGTCACAAGT GAGTTATAAAA GGGTCGCACG chr21_31710037_31710087_ 15 5.94e-05 CCCAGGTTTC TGAGTATATAA TCGCCGCACC chr21_36411748_36411798_ 23 6.78e-05 AGTTTCAGTT GGCATCtaaaa attatataac chr21_31933633_31933683_ 3 2.08e-04 TC AGAGTATATAT AAATGTTCCT chr21_31962741_31962791_ 14 4.05e-04 TATAACTCAG GTTGGATAAAA TAATTTGTAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr21_46046964_46047014_ 1.1e-06 12_[1]_27 chr21_46057197_46057247_ 3.4e-06 36_[1]_3 chr21_45971413_45971463_ 3.4e-06 9_[1]_30 chr21_31964683_31964733_ 3.4e-06 13_[1]_26 chr21_45993530_45993580_ 4e-06 7_[1]_32 chr21_32202076_32202126_ 5e-06 13_[1]_26 chr21_46031920_46031970_ 6.1e-06 15_[1]_24 chr21_32410820_32410870_ 8.7e-06 21_[1]_18 chr21_32185595_32185645_ 8.7e-06 18_[1]_21 chr21_31992870_31992920_ 8.7e-06 16_[1]_23 chr21_46020421_46020471_ 1.2e-05 2_[1]_37 chr21_47517957_47518007_ 1.6e-05 32_[1]_7 chr21_45978668_45978718_ 1.6e-05 4_[1]_35 chr21_31914206_31914256_ 1.7e-05 15_[1]_24 chr21_32253899_32253949_ 2e-05 19_[1]_20 chr21_31744582_31744632_ 3.1e-05 12_[1]_27 chr21_19617074_19617124_ 3.1e-05 39_[1] chr21_45705687_45705737_ 3.8e-05 37_[1]_2 chr21_31768316_31768366_ 3.8e-05 [1]_39 chr21_47575506_47575556_ 4e-05 30_[1]_9 chr21_26934381_26934431_ 5.5e-05 27_[1]_12 chr21_31710037_31710087_ 5.9e-05 14_[1]_25 chr21_36411748_36411798_ 6.8e-05 22_[1]_17 chr21_31933633_31933683_ 0.00021 2_[1]_37 chr21_31962741_31962791_ 0.0004 13_[1]_26 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGGGTATAAAA width=11 seqs=25 chr21_46046964_46047014_ ( 13) GGGGTATAAAA 1 chr21_46057197_46057247_ ( 37) GGCATATAAAA 1 chr21_45971413_45971463_ ( 10) GGCATATAAAA 1 chr21_31964683_31964733_ ( 14) GGCATATAAAA 1 chr21_45993530_45993580_ ( 8) GGAGTATAAAA 1 chr21_32202076_32202126_ ( 14) GAGGTATAAAA 1 chr21_46031920_46031970_ ( 16) AGGGTATAAAA 1 chr21_32410820_32410870_ ( 22) GATGTATAAAA 1 chr21_32185595_32185645_ ( 19) GGGATATATAA 1 chr21_31992870_31992920_ ( 17) GATGTATAAAA 1 chr21_46020421_46020471_ ( 3) GACATATAAAA 1 chr21_47517957_47518007_ ( 33) GGGGTATAAAG 1 chr21_45978668_45978718_ ( 5) GGGGTATAAAG 1 chr21_31914206_31914256_ ( 16) AGAGTATAAAA 1 chr21_32253899_32253949_ ( 20) GATATATAAAA 1 chr21_31744582_31744632_ ( 13) AGCATATATAA 1 chr21_19617074_19617124_ ( 40) TGGGTATATAA 1 chr21_45705687_45705737_ ( 38) GGGGTATAACA 1 chr21_31768316_31768366_ ( 1) AACGTATATAA 1 chr21_47575506_47575556_ ( 31) AGCGTATAAAG 1 chr21_26934381_26934431_ ( 28) GAGTTATAAAA 1 chr21_31710037_31710087_ ( 15) TGAGTATATAA 1 chr21_36411748_36411798_ ( 23) GGCATCTAAAA 1 chr21_31933633_31933683_ ( 3) AGAGTATATAT 1 chr21_31962741_31962791_ ( 14) GTTGGATAAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 11 n= 1200 bayes= 5.33554 E= 2.4e-011 -32 -680 91 77 7 138 -20 55 64 107 11 150 142 72 87 396 -148 221 -140 -36 -11 -680 89 76 7 137 -21 55 63 107 10 149 141 71 87 396 -239 220 -140 -36 -79 41 4 21 -7 44 -62 42 -5 99 0 99 138 52 42 399 -46 223 -173 -68 11 -677 48 47 -2 127 -43 46 27 101 3 124 138 60 62 397 -235 220 -160 -55 -596 -820 12 -21 -53 -267 -74 37 16 44 -37 98 31 9 19 319 212 127 -193 -95 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8 -838 -990 -89 -149 -151 -841 -161 -117 -113 -66 -209 -68 -69 -129 -91 111 221 -55 -255 -173 176 -858 -79 -103 -115 -717 -148 -95 -108 -17 -162 -61 -12 -95 -69 193 -737 52 -240 -153 134 -686 0 16 -12 -553 -68 44 -8 96 -9 88 124 41 36 384 11 216 -177 -71 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8 147 -614 89 129 93 -121 12 160 113 217 108 144 144 111 125 447 -241 332 -81 22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 11 nsites= 25 E= 2.4e-011 0.240000 0.000000 0.000000 0.000000 0.000000 0.680000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.080000 0.000000 0.000000 0.000000 0.280000 0.000000 0.000000 0.000000 0.000000 0.680000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 0.160000 0.320000 0.000000 0.000000 0.000000 0.360000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.160000 0.000000 0.000000 0.000000 0.320000 0.000000 0.000000 0.000000 0.000000 0.640000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.960000 0.000000 0.000000 0.000000 0.960000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.760000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.240000 0.000000 0.000000 0.000000 0.960000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.840000 0.000000 0.000000 0.000000 0.000000 0.120000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 regular expression -------------------------------------------------------------------------------- [GA][GA][GC][GA]TATA[AT]AA -------------------------------------------------------------------------------- Time 0.77 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr21_19617074_19617124_ 1.22e-03 39_[1(3.06e-05)] chr21_26934381_26934431_ 2.21e-03 27_[1(5.52e-05)]_12 chr21_28217753_28217803_ 7.29e-01 50 chr21_31710037_31710087_ 2.37e-03 14_[1(5.94e-05)]_25 chr21_31744582_31744632_ 1.22e-03 12_[1(3.06e-05)]_27 chr21_31768316_31768366_ 1.53e-03 [1(3.82e-05)]_39 chr21_31914206_31914256_ 6.70e-04 15_[1(1.68e-05)]_24 chr21_31933633_31933683_ 1.81e-03 4_[1(4.54e-05)]_35 chr21_31962741_31962791_ 1.61e-02 50 chr21_31964683_31964733_ 1.36e-04 13_[1(3.41e-06)]_26 chr21_31973364_31973414_ 1.99e-01 50 chr21_31992870_31992920_ 3.47e-04 16_[1(8.67e-06)]_23 chr21_32185595_32185645_ 3.47e-04 18_[1(8.67e-06)]_21 chr21_32202076_32202126_ 2.01e-04 13_[1(5.01e-06)]_26 chr21_32253899_32253949_ 8.11e-04 19_[1(2.03e-05)]_20 chr21_32410820_32410870_ 3.47e-04 21_[1(8.67e-06)]_18 chr21_36411748_36411798_ 2.71e-03 22_[1(6.78e-05)]_17 chr21_37838750_37838800_ 8.23e-02 50 chr21_45705687_45705737_ 1.53e-03 37_[1(3.82e-05)]_2 chr21_45971413_45971463_ 1.36e-04 9_[1(3.41e-06)]_30 chr21_45978668_45978718_ 6.37e-04 4_[1(1.59e-05)]_35 chr21_45993530_45993580_ 1.60e-04 7_[1(4.00e-06)]_32 chr21_46020421_46020471_ 4.83e-04 2_[1(1.21e-05)]_37 chr21_46031920_46031970_ 2.43e-04 15_[1(6.06e-06)]_24 chr21_46046964_46047014_ 4.26e-05 12_[1(1.06e-06)]_27 chr21_46057197_46057247_ 1.36e-04 36_[1(3.41e-06)]_3 chr21_46086869_46086919_ 4.30e-02 50 chr21_46102103_46102153_ 4.30e-02 50 chr21_47517957_47518007_ 6.37e-04 32_[1(1.59e-05)]_7 chr21_47575506_47575556_ 1.61e-03 30_[1(4.02e-05)]_9 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (1) found. ******************************************************************************** CPU: ThinkPad-T450s ********************************************************************************