<?xml version="1.0" encoding="UTF-8"?>
<!--WARNING: Do not change anything inside this workflow file. BioExtract won't recognize your changes, or may even refuse to import it. Instead, modify the workflow in BioExtract after importing. This workflow file can be imported into BioExtract only.-->
  <s:bioextract xmlns:s="http://bioextract.org" version="2.1" log="0">
<s:workflowdescription description="Designed from an example workflow at Traverna, this workflow retrieves a set of sequences from UniProt, then simultaneously scans for transmembrane regions and performs a multiple alignment using EMMA. The alignment is then plotted to a set of PNG images, followed by a profile analysis using prophecy and prophet tools." author="clushbou@gmail.com" uid="683219f6-4e97-4be3-bda5-9276b4008b89" title="Multiple Protein Alignment Profiling(1)"/>
<s:processor name="query"><s:stringconstant>EB-EYE:uniprot:opsin-2</s:stringconstant></s:processor><s:processor name="emma"><s:description>"Multiple sequence alignment (ClustalW wrapper)"</s:description><s:helpurl>"http://emboss.sourceforge.net/apps/release/6.0/emboss/apps/emma.html"</s:helpurl><s:parameter name="pwmatrix" value="b"/><s:parameter name="pwdnamatrix" value="i"/><s:parameter name="matrix" value="b"/><s:parameter name="dnamatrix" value="i"/><s:parameter name="pwgapopen" value="10.0"/><s:parameter name="pwgapextend" value="0.1"/><s:parameter name="gapopen" value="10.0"/><s:parameter name="gapextend" value="5.0"/><s:parameter name="gapdist" value="8"/><s:parameter name="hgapres" value="GPSNDQEKR"/><s:parameter name="maxdiv" value="30"/><s:parameter name="osformat_outseq" value="fasta"/></s:processor><s:processor name="tmap"><s:description>"Predict and plot transmembrane segments in protein sequences"</s:description><s:helpurl>"http://emboss.sourceforge.net/apps/release/6.0/emboss/apps/tmap.html"</s:helpurl><s:parameter name="graph_format" value="png"/></s:processor><s:processor name="prettyplot"><s:description>"Draw a sequence alignment with pretty formatting"</s:description><s:helpurl>"http://emboss.sourceforge.net/apps/release/4.1/emboss/apps/prettyplot.html"</s:helpurl><s:parameter name="graph_format" value="png"/><s:parameter name="residuesperline" value="50"/><s:parameter name="cidentity" value="RED"/><s:parameter name="csimilarity" value="GREEN"/><s:parameter name="cother" value="BLACK"/><s:parameter name="pair" value="1.5,1.0,0.5"/><s:parameter name="identity" value="0"/><s:parameter name="boxuse" value="GREY"/><s:parameter name="maxnamelen" value="10"/><s:parameter name="alternative" value="0"/><s:parameter name="showscore" value="-1"/></s:processor><s:processor name="prophecy"><s:description>"Create frequency matrix or profile from a multiple alignment"</s:description><s:helpurl>"http://emboss.sourceforge.net/apps/release/6.0/emboss/apps/prophecy.html"</s:helpurl><s:parameter name="type" value="G"/><s:parameter name="name" value="mymatrix"/><s:parameter name="threshold" value="75"/><s:parameter name="open" value="3.0"/><s:parameter name="extension" value="0.3"/></s:processor><s:processor name="query"><s:stringconstant>EB-EYE:emblnew_standard:L07770</s:stringconstant><s:stringconstant>EB-EYE:emblrelease_standard:L07770</s:stringconstant></s:processor><s:processor name="transeq"><s:description>"Translate nucleic acid sequences"</s:description><s:helpurl>"http://emboss.sourceforge.net/apps/release/6.0/emboss/apps/transeq.html"</s:helpurl><s:parameter name="frame_1" value="checkbox-on"/><s:parameter name="table" value="0"/><s:parameter name="osformat_outseq" value="fasta"/></s:processor><s:processor name="prophet"><s:description>"Scan one or more sequences with a Gribskov or Henikoff profile"</s:description><s:helpurl>"http://emboss.sourceforge.net/apps/release/6.0/emboss/apps/prophet.html"</s:helpurl><s:parameter name="gapopen" value="1.0"/><s:parameter name="gapextend" value="1.0"/></s:processor><s:link source="query:value" sink="emma:sequence_usa" />
<s:link source="emma:outseq" sink="tmap:sequences_direct_data" />
 <s:link source="tmap:Graphics_in_PNG" sink="tmap" />
<s:sink name="tmap">
 <s:metadata> <s:mimeTypes>
<s:mimeType>image/png</s:mimeType>
 </s:mimeTypes> </s:metadata> </s:sink>
  </s:bioextract>