<?xml version='1.0' encoding='UTF-8' standalone='yes'?>
<!-- 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
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xsi:schemaLocation="http://zlab.bu.edu/schema/cisml cisml.xsd"
  xmlns:mem="http://noble.gs.washington.edu/meme"
>
<program-name>ama</program-name>
<parameters>
<command-line>ama --pvalues --verbosity 1 --cs /Users/t.bailey/meme_git/meme/tests/gomo/motif.meme.txt /Users/t.bailey/meme_git/meme/tests/gomo/seqs_red.fasta /Users/t.bailey/meme_git/meme/tests/gomo/seqs.norc.bg</command-line>
<pattern-file>/Users/t.bailey/meme_git/meme/tests/gomo/motif.meme.txt</pattern-file>
<sequence-file>/Users/t.bailey/meme_git/meme/tests/gomo/seqs_red.fasta</sequence-file>
<background-seq-file>/Users/t.bailey/meme_git/meme/tests/gomo/seqs.norc.bg</background-seq-file>
<sequence-filtering on-off="off"/>
</parameters>
<pattern accession="HSF1" name="">
<scanned-sequence accession="S000000001" name="S000000001" score="0.0182431" pvalue="0.695216" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000002" name="S000000002" score="4.01114e-06" pvalue="0.673615" length="40">
</scanned-sequence>
</pattern>
<pattern accession="RPN4" name="">
<scanned-sequence accession="S000000001" name="S000000001" score="0.000763757" pvalue="0.741525" length="1000">
</scanned-sequence>
<scanned-sequence accession="S000000002" name="S000000002" score="4.71901e-06" pvalue="0.329112" length="40">
</scanned-sequence>
</pattern>
</cis-element-search>
