<?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="Query with the NCBI Protein Database, Blastp, ClustalW, Transeq, Garnier, PepWindowWall, PepInfo, Octanol" author="Kendra Giesey" uid="2603f97a-65d7-4db4-9dca-50926e6421e6" title="Protein Mutation"/>
<s:processor name="query"><s:stringconstant>NCBI GenBank Protein:NP_000491.2</s:stringconstant></s:processor><s:processor name="blastp"><s:description>"Search a protein database using a protein query"</s:description><s:helpurl>"http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs"</s:helpurl><s:parameter name="Select database" value="nr"/><s:parameter name="Do CD-Search" value="checkbox-on"/><s:parameter name="Limit to the organism" value="All organisms"/><s:parameter name="Expect" value="10"/><s:parameter name="Word size" value="w_3"/><s:parameter name="Matrix" value="BLOSUM62"/><s:parameter name="Gap costs" value="Existence_11_Extension_1"/><s:parameter name="Filter: Low-complexity" value="checkbox-on"/><s:parameter name="Show graphical overview" value="checkbox-on"/><s:parameter name="Show database linkouts" value="checkbox-on"/><s:parameter name="Number of descriptions" value="d_100"/><s:parameter name="Number of alignments" value="a_100"/><s:parameter name="maximum number of sequences" value="100"/></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="transeq"><s:description>"Translate nucleic acid sequences"</s:description><s:soaplabwsdl>http://www.ebi.ac.uk/soaplab/services/nucleic_translation.transeq</s:soaplabwsdl><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="garnier"><s:description>"Predicts protein secondary structure using GOR method"</s:description><s:soaplabwsdl>http://www.ebi.ac.uk/soaplab/services/protein_2d_structure.garnier</s:soaplabwsdl><s:helpurl>"http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/garnier.html"</s:helpurl><s:parameter name="idc" value="0"/></s:processor><s:processor name="pepwindowall"><s:description>"Draw Kyte-Doolittle hydropathy plot for a protein alignment"</s:description><s:soaplabwsdl>http://www.ebi.ac.uk/soaplab/services/protein_composition.pepwindowall</s:soaplabwsdl><s:helpurl>"http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/pepwindowall.html"</s:helpurl><s:parameter name="graph_format" value="png"/><s:parameter name="length" value="19"/></s:processor><s:processor name="pepinfo"><s:description>"Plot amino acid properties of a protein sequence in parallel."</s:description><s:soaplabwsdl>http://www.ebi.ac.uk/soaplab/services/protein_composition.pepinfo</s:soaplabwsdl><s:helpurl>"http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/pepinfo.html"</s:helpurl><s:parameter name="graph_format" value="png"/><s:parameter name="hwindow" value="9"/></s:processor><s:processor name="octanol"><s:description>"Draw a White-Wimley protein hydropathy plot"</s:description><s:soaplabwsdl>http://www.ebi.ac.uk/soaplab/services/protein_composition.octanol</s:soaplabwsdl><s:helpurl>"http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/octanol.html"</s:helpurl><s:parameter name="graph_format" value="png"/><s:parameter name="width" value="19"/></s:processor><s:link source="query:value" sink="blastp:sequence_usa" />
<s:link source="blastp:outseq" sink="ClustalW:sequences_direct_data" />
 <s:link source="ClustalW:Graphics_in_PNG" sink="ClustalW" />
<s:sink name="ClustalW">
 <s:metadata> <s:mimeTypes>
<s:mimeType>image/png</s:mimeType>
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  </s:bioextract>