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1 application: gbui [
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2 documentation: "Calculates base usage indices for protein-coding sequences"
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3 groups: "Nucleic:Codon usage"
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4 embassy: "gembassy"
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5 relations: "EDAM_topic:0157 Sequence composition analysis"
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6 relations: "EDAM_operation:0236 Sequence composition calculation"
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7 relations: "EDAM_operation:0377 Sequence composition calculation
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8 (nucleic acid)"
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9 ]
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10
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11 section: input [
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12 information: "Input section"
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13 type: "page"
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14 ]
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15
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16 seqall: sequence [
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17 parameter: "Y"
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18 type: "nucleotide"
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19 features: "Y"
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20 relations: "EDAM_data:0849 Sequence record"
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21 ]
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22
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23 endsection: input
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24
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25 section: advanced [
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26 information: "Advanced section"
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27 type: "page"
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28 ]
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29
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30 boolean: translate [
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31 information: "Include when translating using standard codon table"
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32 default: "N"
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33 ]
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34
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35 list: position [
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36 information: "Codon position"
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37 values: "all: Assess overall base usage of the gene;
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38 1: Assess base usage at 1st position of codons;
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39 2: Assess base usage at 2nd position of codons;
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40 3: Assess base usage at 3rd position of codons"
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41 default: "all"
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42 ]
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43
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44 string: delkey [
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45 information: "Regular expression to delete key"
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46 knowntype: "regular expression"
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47 default: "[^ACDEFGHIKLMNPQRSTVWYacgtU]"
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48 ]
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49
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50 boolean: accid [
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51 information: "Include to use sequence accession ID as query"
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52 default: "N"
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53 ]
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54
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55 endsection: advanced
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56
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57 section: output [
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58 information: "Output section"
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59 type: "page"
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60 ]
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61
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62 outfile: outfile [
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63 parameter: "Y"
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64 information: "Program compseq output file"
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65 knowntype: "compseq output"
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66 relations: "EDAM_data:3086 Nucleic acid sequence composition"
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67 ]
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68
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69 endsection: output
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