Mercurial > repos > iuc > meme_dreme

comparison test-data/dreme_fimo_input_1.xml @ 1:cb8a2242bf03 draft

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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
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0:b386032d758d 1:cb8a2242bf03
1 <dreme version="4.12.0" release="Tue Jun 27 16:22:50 2017 -0700">
2 <model>
3 <command_line>dreme -oc dreme_out -norc -p input.fa</command_line>
4 <positives name="input" count="1000" file="input.fa" last_mod_date="Wed May 02 16:37:00 CEST 2018" />
5 <negatives name="shuffled positive sequences" count="1000" from="shuffled"/>
6 <alphabet name="DNA" like="dna">
7 <letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/>
8 <letter id="C" symbol="C" complement="G" name="Cytosine" colour="0000CC"/>
9 <letter id="G" symbol="G" complement="C" name="Guanine" colour="FFB300"/>
10 <letter id="T" symbol="T" aliases="U" complement="A" name="Thymine" colour="008000"/>
11 <letter id="N" symbol="N" aliases="X." equals="ACGT" name="Any base"/>
12 <letter id="V" symbol="V" equals="ACG" name="Not T"/>
13 <letter id="H" symbol="H" equals="ACT" name="Not G"/>
14 <letter id="D" symbol="D" equals="AGT" name="Not C"/>
15 <letter id="B" symbol="B" equals="CGT" name="Not A"/>
16 <letter id="M" symbol="M" equals="AC" name="Amino"/>
17 <letter id="R" symbol="R" equals="AG" name="Purine"/>
18 <letter id="W" symbol="W" equals="AT" name="Weak"/>
19 <letter id="S" symbol="S" equals="CG" name="Strong"/>
20 <letter id="Y" symbol="Y" equals="CT" name="Pyrimidine"/>
21 <letter id="K" symbol="K" equals="GT" name="Keto"/>
22 </alphabet>
23 <strands>given</strands>
24 <background A="0.294" C="0.209" G="0.164" T="0.333" from="dataset"/>
25 <stop evalue="0.05"/>
26 <ngen>100</ngen>
27 <add_pv_thresh>0.01</add_pv_thresh>
28 <seed>1</seed>
29 <host>ThinkPad-T450s</host>
30 <when>Wed May 02 16:45:34 CEST 2018</when>
31 </model>
32 <motifs>
33 <motif id="m01" alt="DREME-1" seq="ACTAAYH" length="7" nsites="405" p="371" n="75" pvalue="9.7e-061" evalue="4.9e-056" unerased_evalue="4.9e-056">
34 <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/>
35 <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/>
36 <pos A="0.000000" C="0.000000" G="0.000000" T="1.000000"/>
37 <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/>
38 <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/>
39 <pos A="0.000000" C="0.600000" G="0.000000" T="0.400000"/>
40 <pos A="0.471605" C="0.244444" G="0.000000" T="0.283951"/>
41 <match seq="ACTAACA" p="108" n="10" pvalue="2.6e-023" evalue="1.3e-018"/>
42 <match seq="ACTAACC" p="62" n="7" pvalue="9.5e-013" evalue="4.8e-008"/>
43 <match seq="ACTAATA" p="77" n="18" pvalue="1.5e-010" evalue="7.4e-006"/>
44 <match seq="ACTAACT" p="62" n="16" pvalue="4.4e-008" evalue="2.2e-003"/>
45 <match seq="ACTAATC" p="35" n="8" pvalue="1.7e-005" evalue="8.8e-001"/>
46 <match seq="ACTAATT" p="48" n="20" pvalue="3.7e-004" evalue="1.9e+001"/>
47 </motif>
48 <motif id="m02" alt="DREME-2" seq="YTAACA" length="6" nsites="197" p="170" n="59" pvalue="1.8e-015" evalue="9.0e-011" unerased_evalue="6.8e-031">
49 <pos A="0.000000" C="0.365482" G="0.000000" T="0.634518"/>
50 <pos A="0.000000" C="0.000000" G="0.000000" T="1.000000"/>
51 <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/>
52 <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/>
53 <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/>
54 <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/>
55 <match seq="TTAACA" p="118" n="38" pvalue="8.6e-012" evalue="4.3e-007"/>
56 <match seq="CTAACA" p="63" n="21" pvalue="1.6e-006" evalue="7.8e-002"/>
57 </motif>
58 <motif id="m03" alt="DREME-3" seq="TCTGT" length="5" nsites="220" p="208" n="101" pvalue="1.9e-011" evalue="9.2e-007" unerased_evalue="4.4e-007">
59 <pos A="0.000000" C="0.000000" G="0.000000" T="1.000000"/>
60 <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/>
61 <pos A="0.000000" C="0.000000" G="0.000000" T="1.000000"/>
62 <pos A="0.000000" C="0.000000" G="1.000000" T="0.000000"/>
63 <pos A="0.000000" C="0.000000" G="0.000000" T="1.000000"/>
64 <match seq="TCTGT" p="208" n="101" pvalue="1.9e-011" evalue="9.2e-007"/>
65 </motif>
66 <motif id="m04" alt="DREME-4" seq="SCCAGG" length="6" nsites="58" p="58" n="14" pvalue="5.0e-008" evalue="2.4e-003" unerased_evalue="1.5e-003">
67 <pos A="0.000000" C="0.620690" G="0.379310" T="0.000000"/>
68 <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/>
69 <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/>
70 <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/>
71 <pos A="0.000000" C="0.000000" G="1.000000" T="0.000000"/>
72 <pos A="0.000000" C="0.000000" G="1.000000" T="0.000000"/>
73 <match seq="CCCAGG" p="36" n="9" pvalue="2.7e-005" evalue="1.3e+000"/>
74 <match seq="GCCAGG" p="22" n="5" pvalue="7.1e-004" evalue="3.4e+001"/>
75 </motif>
76 <motif id="m05" alt="DREME-5" seq="CCAGCAY" length="7" nsites="27" p="27" n="1" pvalue="9.2e-008" evalue="4.4e-003" unerased_evalue="2.3e-003">
77 <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/>
78 <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/>
79 <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/>
80 <pos A="0.000000" C="0.000000" G="1.000000" T="0.000000"/>
81 <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/>
82 <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/>
83 <pos A="0.000000" C="0.518519" G="0.000000" T="0.481481"/>
84 <match seq="CCAGCAC" p="14" n="0" pvalue="5.8e-005" evalue="2.8e+000"/>
85 <match seq="CCAGCAT" p="13" n="1" pvalue="8.9e-004" evalue="4.3e+001"/>
86 </motif>
87 <motif id="m06" alt="DREME-6" seq="GMATGT" length="6" nsites="60" p="59" n="18" pvalue="9.9e-007" evalue="4.8e-002" unerased_evalue="4.8e-002">
88 <pos A="0.000000" C="0.000000" G="1.000000" T="0.000000"/>
89 <pos A="0.533333" C="0.466667" G="0.000000" T="0.000000"/>
90 <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/>
91 <pos A="0.000000" C="0.000000" G="0.000000" T="1.000000"/>
92 <pos A="0.000000" C="0.000000" G="1.000000" T="0.000000"/>
93 <pos A="0.000000" C="0.000000" G="0.000000" T="1.000000"/>
94 <match seq="GCATGT" p="28" n="8" pvalue="5.4e-004" evalue="2.6e+001"/>
95 <match seq="GAATGT" p="32" n="11" pvalue="8.6e-004" evalue="4.1e+001"/>
96 </motif>
97 </motifs>
98 <run_time cpu="30.86" real="30.97" stop="evalue"/>
99 </dreme>