<?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="Please enter a workflow description." author="Xiaozhu Zhang" uid="3125F648-6EA7-65C2-AE2F-18DE1A1C44A0" title="SH2 domain (in homo) screen"/>
<s:processor name="query"><s:stringconstant>NCBI GenBank Protein:SH2 AND Organism=homo AND NOT Definition=binding AND NOT Definition=chain</s:stringconstant></s:processor><s:processor name="xmknr"><s:description>"Reads multiple sequence records in FASTA format and removes duplicates"</s:description><s:helpurl>"http://www.vmatch.de/"</s:helpurl><s:parameter name="Sequence type (protein or DNA)" value="protein"/><s:parameter name="Minimum sequence length to include" value="1"/><s:parameter name="xdrop value for edit distance" value="2"/><s:parameter name="Small cluster value" value="90"/><s:parameter name="Large cluster value" value="90"/></s:processor><s:processor name="FormatConversion"><s:description>"Convert from one allowed format to another allowed format"</s:description><s:helpurl>"http://emboss.sourceforge.net/docs/themes/SequenceFormats.html"</s:helpurl><s:parameter name="To Format" value="embl"/><s:parameter name="From Format" value="genbank"/></s:processor><s:processor name="extractfeat"><s:description>"Extract features from sequence(s)"</s:description><s:soaplabwsdl>http://www.ebi.ac.uk/soaplab/services/edit.extractfeat</s:soaplabwsdl><s:helpurl>"http://emboss.sourceforge.net/apps/release/4.1/emboss/apps/extractfeat.html"</s:helpurl><s:parameter name="before" value="0"/><s:parameter name="after" value="0"/><s:parameter name="type" value="region"/><s:parameter name="sense" value="0"/><s:parameter name="minscore" value="0.0"/><s:parameter name="maxscore" value="0.0"/><s:parameter name="value" value="*SH2*"/><s:parameter name="osformat_outseq" value="fasta"/></s:processor><s:processor name="sizeseq"><s:description>"Sort sequences by size"</s:description><s:soaplabwsdl>http://www.ebi.ac.uk/soaplab/services/edit.sizeseq</s:soaplabwsdl><s:helpurl>"http://emboss.sourceforge.net/apps/release/4.1/emboss/apps/sizeseq.html"</s:helpurl><s:parameter name="descending" value="checkbox-on"/><s:parameter name="osformat_outseq" value="fasta"/></s:processor><s:processor name="skipseq"><s:description>"Reads and writes (returns) sequences,                  skipping first few"</s:description><s:soaplabwsdl>http://www.ebi.ac.uk/soaplab/services/edit.skipseq</s:soaplabwsdl><s:helpurl>"http://emboss.sourceforge.net/apps/release/4.1/emboss/apps/skipseq.html"</s:helpurl><s:parameter name="skip" value="14"/><s:parameter name="osformat_outseq" value="fasta"/></s:processor><s:processor name="sizeseq"><s:description>"Sort sequences by size"</s:description><s:soaplabwsdl>http://www.ebi.ac.uk/soaplab/services/edit.sizeseq</s:soaplabwsdl><s:helpurl>"http://emboss.sourceforge.net/apps/release/4.1/emboss/apps/sizeseq.html"</s:helpurl><s:parameter name="osformat_outseq" value="fasta"/></s:processor><s:processor name="skipseq"><s:description>"Reads and writes (returns) sequences,                  skipping first few"</s:description><s:soaplabwsdl>http://www.ebi.ac.uk/soaplab/services/edit.skipseq</s:soaplabwsdl><s:helpurl>"http://emboss.sourceforge.net/apps/release/4.1/emboss/apps/skipseq.html"</s:helpurl><s:parameter name="skip" value="6"/><s:parameter name="osformat_outseq" value="fasta"/></s:processor><s:processor name="skipredundant"><s:description>"Remove redundant sequences from an input set"</s:description><s:soaplabwsdl>http://www.ebi.ac.uk/soaplab/services/edit.skipredundant</s:soaplabwsdl><s:helpurl>"http://emboss.sourceforge.net/apps/release/4.1/emboss/apps/skipredundant.html"</s:helpurl><s:parameter name="mode" value="1"/><s:parameter name="threshold" value="95.0"/><s:parameter name="minthreshold" value="30.0"/><s:parameter name="maxthreshold" value="90.0"/><s:parameter name="osformat_outseq" value="fasta"/><s:parameter name="osformat_redundantoutseq" value="fasta"/></s:processor><s:processor name="emma"><s:description>"Multiple sequence alignment (ClustalW wrapper)"</s:description><s:soaplabwsdl>http://www.ebi.ac.uk/soaplab/services/alignment_multiple.emma</s:soaplabwsdl><s:helpurl>"http://emboss.sourceforge.net/apps/release/4.1/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="prettyplot"><s:description>"Draw a sequence alignment with pretty formatting"</s:description><s:soaplabwsdl>http://www.ebi.ac.uk/soaplab/services/display.prettyplot</s:soaplabwsdl><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="boxcolval" 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:soaplabwsdl>http://www.ebi.ac.uk/soaplab/services/nucleic_profiles.prophecy</s:soaplabwsdl><s:helpurl>"http://emboss.sourceforge.net/apps/release/4.1/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="ClustalW"><s:description>"Multiple sequence alignment for DNA or proteins"</s:description><s:helpurl>"http://align.genome.jp/clustalw/clustalw_help.html"</s:helpurl><s:parameter name="Output format" value="clu"/><s:parameter name="Pairwise alignment" value="fast"/><s:parameter name="Sequence type" value="protein"/><s:parameter name="K-tuple(word) size" value="1"/><s:parameter name="Window size" value="5"/><s:parameter name="Gap penalty" value="3"/><s:parameter name="Number of top diagonals" value="5"/><s:parameter name="Scoring method" value="percent"/><s:parameter name="Gap open penalty" value="10"/><s:parameter name="Gap extension penalty" value="0.1"/><s:parameter name="Select weight matrix" value="blosum"/></s:processor><s:processor name="query"><s:stringconstant>NCBI GenBank Protein:Q96JZ2</s:stringconstant></s:processor><s:processor name="prophet"><s:description>"Scan one or more sequences with a Gribskov                  or Henikoff profile"</s:description><s:soaplabwsdl>http://www.ebi.ac.uk/soaplab/services/nucleic_profiles.prophet</s:soaplabwsdl><s:helpurl>"http://emboss.sourceforge.net/apps/release/4.1/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="xmknr:sequence_usa" />
<s:link source="xmknr:outseq" sink="FormatConversion:sequences_direct_data" />
 <s:link source="FormatConversion:Graphics_in_PNG" sink="FormatConversion" />
<s:sink name="FormatConversion">
 <s:metadata> <s:mimeTypes>
<s:mimeType>image/png</s:mimeType>
 </s:mimeTypes> </s:metadata> </s:sink>
  </s:bioextract>