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1 application: gcbi [
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2 documentation: "Calculates the codon bias index (CBI)"
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3 groups: "Nucleic:Codon usage"
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4 embassy: "gembassy"
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5 relations: "EDAM_operation:0286 Codon usage analysis"
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6 relations: "EDAM_topic:0107 Codon usage analysis"
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7 ]
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8
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9 section: input [
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10 information: "Input section"
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11 type: "page"
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12 ]
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13
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14 seqall: sequence [
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15 parameter: "Y"
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16 type: "nucleotide"
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17 features: "Y"
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18 relations: "EDAM_data:0849 Sequence record"
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19 ]
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20
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21 endsection: input
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22
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23 section: advanced [
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24 information: "Advanced section"
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25 type: "page"
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26 ]
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27
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28 boolean: translate [
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29 information: "Include when translating using standard codon table"
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30 default: "N"
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31 ]
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32
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33 string: delkey [
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34 information: "Regular expression to delete key"
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35 knowntype: "regular expression"
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36 default: "[^ACDEFGHIKLMNPQRSTVWYacgtU]"
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37 ]
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38
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39 boolean: accid [
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40 information: "Include to use sequence accession ID as query"
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41 default: "N"
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42 ]
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43
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44 endsection: advanced
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45
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46 section: output [
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47 information: "Output section"
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48 type: "page"
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49 ]
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50
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51 outfile: outfile [
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52 parameter: "Y"
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53 information: "Codon usage output file"
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54 knowntype: "codon usage"
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55 relations: "EDAM_data:2865 Codon usage bias"
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56 ]
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57
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58 endsection: output
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