<?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 carries out alignments using TCoffee and ClustalW2 for a set of non-redundant proteins where the starting point is a particular genomic coding sequence representing only one member of the gene family in a given species. " author="clushbou@gmail.com" uid="0c34e6e0-3c62-4849-a95f-ff27ef127eb2" title="tblastx non-redundant alignment"/>
<s:processor name="query"><s:stringconstant>NCBI:nuccore:L16896</s:stringconstant></s:processor><s:processor name="tblastx"><s:description>"Search translated nucleotide database using a translated 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="Genetic code" value="Standard__1"/><s:parameter name="Limit to the following 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="Descriptions" value="d_50"/><s:parameter name="Alignments" value="a_50"/><s:parameter name="maximum number of sequences" value="50"/></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="dna"/><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="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="ClustalW2"><s:description>"Multiple Sequence Alignments"</s:description><s:helpurl>"http://www.clustal.org/download/clustalw_help.txt"</s:helpurl><s:parameter name="Output format" value="clustal"/><s:parameter name="Sequence type" value="protein"/><s:parameter name="Pairwise alignment" value="fast"/><s:parameter name="Scoring method" value="percent"/><s:parameter name="Select weight matrix" value="blosum"/></s:processor><s:processor name="TCoffee"><s:description>"Computes a multiple sequence alignment and the associated phylogenetic tree for Protein, RNA and DNA sequences"</s:description><s:helpurl>"http://www.tcoffee.org/"</s:helpurl><s:parameter name="Matrix series to use" value="blosum"/><s:parameter name="Order in which seqs appear in final alignment" value="aligned"/></s:processor><s:link source="query:value" sink="tblastx:sequence_usa" />
<s:link source="tblastx:outseq" sink="xmknr:sequences_direct_data" />
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<s:sink name="xmknr">
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