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<!-- Document definition -->
<!-- http://zlab.bu.edu/~phaverty/SupplementalData/CisML/cisml.dtd -->
<!DOCTYPE cis-element-search[
<!ELEMENT cis-element-search (program-name, parameters, (pattern | multi-pattern-scan)*)>
<!ELEMENT program-name (#PCDATA)>
<!ELEMENT parameters (
  pattern-file, 
  sequence-file, 
  background-seq-file?,
  pattern-pvalue-cutoff?,
  sequence-pvalue-cutoff?,
  site-pvalue-cutoff?,
  sequence-filtering,
  ANY*
 )>
<!ELEMENT command-line (#PCDATA)>
<!ELEMENT pattern-file (#PCDATA)>
<!ELEMENT sequence-file (#PCDATA)>
<!ELEMENT background-seq-file (#PCDATA)>
<!ELEMENT pattern-pvalue-cutoff (#PCDATA)>
<!ELEMENT sequence-pvalue-cutoff (#PCDATA)>
<!ELEMENT site-pvalue-cutoff (#PCDATA)>
<!ELEMENT sequence-filtering EMPTY>
<!ELEMENT multi-pattern-scan (pattern+, ANY*)>
<!ELEMENT pattern (scanned-sequence+, ANY*)>
<!ELEMENT scanned-sequence (matched-element*, ANY*)>
<!ELEMENT matched-element (sequence)>
<!ELEMENT sequence (#PCDATA)>
<!ATTLIST cis-element-search
xmlns:xsi CDATA #IMPLIED
xmlns:mem CDATA #IMPLIED
xsi:schemaLocation CDATA #IMPLIED
>
<!ATTLIST sequence-filtering
on-off CDATA #REQUIRED
type CDATA #IMPLIED
>
<!ATTLIST multi-pattern-scan
score CDATA #IMPLIED
pvalue CDATA #IMPLIED
>
<!ATTLIST pattern
accession CDATA #REQUIRED
name CDATA #REQUIRED
pvalue CDATA #IMPLIED
score CDATA #IMPLIED
db CDATA #IMPLIED
lsid CDATA #IMPLIED
>
<!ATTLIST scanned-sequence
accession CDATA #REQUIRED
name CDATA #REQUIRED
score CDATA #IMPLIED
pvalue CDATA #IMPLIED
length CDATA #IMPLIED
db CDATA #IMPLIED
lsid CDATA #IMPLIED
>
<!ATTLIST matched-element
start CDATA #REQUIRED
stop CDATA #REQUIRED
score CDATA #IMPLIED
pvalue CDATA #IMPLIED
clusterid CDATA #IMPLIED
>

]>
<cis-element-search
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  xmlns="http://zlab.bu.edu/schema/cisml"
  xmlns:mem="http://noble.gs.washington.edu/meme"
>
<program-name>fimo</program-name>
<parameters>
<command-line>fimo --verbosity 1 --oc xstreme_example_output_files/fimo_out_9 --bgfile xstreme_example_output_files/background --motif 8-GGTCACGTGABBS xstreme_example_output_files/streme_out/streme.xml nrmix.nseqs.100.100bp.seed.1.fa</command-line>
<pattern-file>xstreme_example_output_files/streme_out/streme.xml</pattern-file>
<sequence-file>nrmix.nseqs.100.100bp.seed.1.fa</sequence-file>
<site-pvalue-cutoff>0.0001</site-pvalue-cutoff>
<sequence-filtering on-off="off"/>
</parameters>
<pattern accession="8-GGTCACGTGABBS" name="STREME-8">
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</scanned-sequence>
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</scanned-sequence>
<scanned-sequence accession="5" name="5">
<matched-element start="43603059" stop="43603047" score="15.3034" pvalue="4.18e-06">
<sequence>GGCCACGTGACTG</sequence>
<mem:qvalue>0.0513</mem:qvalue>
</matched-element>
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<scanned-sequence accession="4" name="4">
<matched-element start="24474453" stop="24474441" score="12.8202" pvalue="2.04e-05">
<sequence>GCCCACGTGACGG</sequence>
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</matched-element>
<matched-element start="24474442" stop="24474454" score="10.9101" pvalue="5.35e-05">
<sequence>CGTCACGTGGGCG</sequence>
<mem:qvalue>0.15</mem:qvalue>
</matched-element>
</scanned-sequence>
<scanned-sequence accession="12" name="12">
<matched-element start="64616163" stop="64616175" score="15.8764" pvalue="2.75e-06">
<sequence>GGTGACGTCATGC</sequence>
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</matched-element>
<matched-element start="64616190" stop="64616178" score="11.8202" pvalue="3.47e-05">
<sequence>GCTGACGTCACGT</sequence>
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</matched-element>
<matched-element start="64616179" stop="64616191" score="10.2472" pvalue="7.15e-05">
<sequence>CGTGACGTCAGCC</sequence>
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<matched-element start="1510426" stop="1510438" score="19.4944" pvalue="2.41e-08">
<sequence>GGTCACGTGACGC</sequence>
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<matched-element start="1510437" stop="1510425" score="14.0899" pvalue="9.62e-06">
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