<?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="This workflow uses a Blastn against the Homo sapiens genome, Blastn against the Mus musculus genome, the Format Conversion Tool, the Fetch Translation Tool, and the ClustalW tool." author="Kendra Giesey" uid="0ed77a26-f25d-40d4-9cc3-287e1f733f0b" title="Phylogenetic Study Using the Bio Extract Server "/>
<s:processor name="query"><s:stringconstant>NCBI GenBank Nucleotide:human AND Gene=HOXD13</s:stringconstant></s:processor><s:processor name="blastn"><s:description>"Search a nucleotide database using a nucleotide 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="Limit by entrez query" value="Homo sapiens"/><s:parameter name="Limit to the following organism" value="Mammalia"/><s:parameter name="Expect" value="10"/><s:parameter name="Word size" value="w_11"/><s:parameter name="Filter: Low-complexity" value="checkbox-on"/><s:parameter name="Filter: Human repeats" value="checkbox-on"/><s:parameter name="Filter: Mask for lookup table only" value="checkbox-on"/><s:parameter name="Number of descriptions" value="d_10"/><s:parameter name="Number of alignments" value="a_10"/><s:parameter name="maximum number of sequences" value="10"/></s:processor><s:processor name="blastn"><s:description>"Search a nucleotide database using a nucleotide 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="Limit by entrez query" value="Mus musculus"/><s:parameter name="Limit to the following organism" value="Mammalia"/><s:parameter name="Expect" value="10"/><s:parameter name="Word size" value="w_11"/><s:parameter name="Filter: Low-complexity" value="checkbox-on"/><s:parameter name="Filter: Human repeats" value="checkbox-on"/><s:parameter name="Filter: Mask for lookup table only" value="checkbox-on"/><s:parameter name="Number of descriptions" value="d_10"/><s:parameter name="Number of alignments" value="a_10"/><s:parameter name="maximum number of sequences" value="10"/></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="genbank"/><s:parameter name="From Format" value="fasta"/></s:processor><s:processor name="FetchTranslation"><s:description>"Extracts translations from feature tables"</s:description><s:helpurl>""</s:helpurl><s:parameter name="Feature name" value="CDS"/><s:parameter name="Qualifier name" value="gene"/></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:link source="query:value" sink="blastn:sequence_usa" />
<s:link source="blastn:outseq" sink="blastn:sequences_direct_data" />
 <s:link source="blastn:Graphics_in_PNG" sink="blastn" />
<s:sink name="blastn">
 <s:metadata> <s:mimeTypes>
<s:mimeType>image/png</s:mimeType>
 </s:mimeTypes> </s:metadata> </s:sink>
  </s:bioextract>