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<!-- Document definition -->
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<!DOCTYPE cis-element-search[
<!ELEMENT cis-element-search (program-name, parameters, (pattern | multi-pattern-scan)*)>
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<!ELEMENT sequence-file (#PCDATA)>
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<!ELEMENT site-pvalue-cutoff (#PCDATA)>
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<!ELEMENT pattern (scanned-sequence+, ANY*)>
<!ELEMENT scanned-sequence (matched-element*, ANY*)>
<!ELEMENT matched-element (sequence)>
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<!ATTLIST cis-element-search
xmlns:xsi CDATA #IMPLIED
xmlns:mem CDATA #IMPLIED
xsi:schemaLocation CDATA #IMPLIED
>
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on-off CDATA #REQUIRED
type CDATA #IMPLIED
>
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score CDATA #IMPLIED
pvalue CDATA #IMPLIED
>
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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
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stop CDATA #REQUIRED
score CDATA #IMPLIED
pvalue CDATA #IMPLIED
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>
<program-name>fimo</program-name>
<parameters>
<command-line>/Users/cegrant/meme_4.12.0/bin/fimo --parse-genomic-coord --verbosity 1 --oc memechip_example_output_files/fimo_out_5 --bgfile memechip_example_output_files/background --motif MA0531.1 JASPAR_CORE_2014.meme memechip_example_output_files/Klf1.fna</command-line>
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<sequence-file>memechip_example_output_files/Klf1.fna</sequence-file>
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