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1 <?xml version='1.0' encoding='UTF-8' standalone='yes'?>
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2 <!DOCTYPE dreme[
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3 <!ELEMENT dreme (model, motifs, run_time)>
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4 <!ATTLIST dreme version CDATA #REQUIRED release CDATA #REQUIRED>
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5 <!ELEMENT model
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6 (command_line, positives, negatives, background, stop, ngen, add_pv_thresh,
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7 seed, host, when, description?)>
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8 <!ELEMENT command_line (#PCDATA)>
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9 <!ELEMENT positives EMPTY>
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10 <!ATTLIST positives
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11 name CDATA #REQUIRED count CDATA #REQUIRED file CDATA #REQUIRED
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12 last_mod_date CDATA #REQUIRED>
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13 <!--
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14 negatives must have a file and last_mod_date specified when the from
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15 attribute is file.
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16 -->
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17 <!ELEMENT negatives EMPTY>
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18 <!ATTLIST negatives
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19 name CDATA #REQUIRED count CDATA #REQUIRED from (shuffled|file) #REQUIRED
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20 file CDATA #IMPLIED last_mod_date CDATA #IMPLIED>
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21 <!--
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22 background allows DNA and RNA (AA is not going to be supported with DREME)
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23 however currently only DNA is implemented. Note that when type is dna the
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24 value for T must be supplied and when the type is rna the value for U must
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25 be supplied. The sum of the frequencies must be 1 (with a small error).
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26 -->
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27 <!ELEMENT background EMPTY>
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28 <!ATTLIST background
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29 type (dna|rna) #REQUIRED
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30 A CDATA #REQUIRED C CDATA #REQUIRED G CDATA #REQUIRED
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31 T CDATA #IMPLIED U CDATA #IMPLIED
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32 from (dataset|file) #REQUIRED
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33 file CDATA #IMPLIED last_mod_date CDATA #IMPLIED>
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34 <!ELEMENT stop EMPTY>
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35 <!ATTLIST stop
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36 evalue CDATA #IMPLIED count CDATA #IMPLIED time CDATA #IMPLIED>
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37 <!ELEMENT ngen (#PCDATA)>
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38 <!ELEMENT seed (#PCDATA)>
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39 <!ELEMENT add_pv_thresh (#PCDATA)>
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40 <!ELEMENT host (#PCDATA)>
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41 <!ELEMENT when (#PCDATA)>
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42 <!ELEMENT description (#PCDATA)>
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43 <!ELEMENT motifs (motif+)>
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44 <!ELEMENT motif (pos+, match+)>
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45 <!ATTLIST motif
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46 id CDATA #REQUIRED seq CDATA #REQUIRED length CDATA #REQUIRED
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47 nsites CDATA #REQUIRED p CDATA #REQUIRED n CDATA #REQUIRED
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48 pvalue CDATA #REQUIRED evalue CDATA #REQUIRED unerased_evalue CDATA #REQUIRED>
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49 <!--
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50 pos allows DNA and RNA (AA is not going to be supported with DREME)
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51 however current only DNA is implemented. When the type in the background
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52 is 'dna' pos must have a T attribute and when it is 'rna' pos must have a
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53 U attribute
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54 -->
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55 <!ELEMENT pos EMPTY>
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56 <!ATTLIST pos
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57 i CDATA #REQUIRED A CDATA #REQUIRED C CDATA #REQUIRED G CDATA #REQUIRED
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58 T CDATA #IMPLIED U CDATA #IMPLIED>
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59 <!ELEMENT match EMPTY>
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60 <!ATTLIST match
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61 seq CDATA #REQUIRED p CDATA #REQUIRED n CDATA #REQUIRED
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62 pvalue CDATA #REQUIRED evalue CDATA #REQUIRED>
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63 <!ELEMENT run_time EMPTY>
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64 <!ATTLIST run_time
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65 cpu CDATA #REQUIRED real CDATA #REQUIRED stop (evalue|count|time) #REQUIRED>
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66 ]>
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67 <dreme version="4.7.0" release="Wed Sep 28 17:30:10 EST 2011">
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68 <model>
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69 <command_line>dreme -p test.fa -desc xxxx</command_line>
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70 <positives name="test" count="3" file="test.fa" last_mod_date="Sat Dec 10 12:52:18 EST 2011" />
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71 <negatives name="shuffled positive sequences" count="3" from="shuffled"/>
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72 <background type="dna" A="0.243" C="0.270" G="0.243" T="0.243" from="dataset"/>
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73 <stop evalue="0.05"/>
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74 <ngen>100</ngen>
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75 <add_pv_thresh>0.01</add_pv_thresh>
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76 <seed>1</seed>
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77 <host>SHARPLAB.MIT.EDU</host>
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78 <when>Sun Dec 11 09:26:43 EST 2011</when>
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79 <description>xxxx</description>
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80 </model>
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81 <motifs>
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82 </motifs>
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83 <run_time cpu="0.01" real="0.01" stop="evalue"/>
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84 </dreme>
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