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1 application: gcodoncompiler [
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2 documentation: "Calculates various kinds of amino acid and codon usage data"
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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 to translate 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 boolean: startcodon [
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34 information: "Include to include start codon"
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35 default: "N"
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36 ]
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37
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38 boolean: stopcodon [
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39 information: "Include to include stop codon"
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40 default: "N"
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41 ]
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42
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43 string: delkey [
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44 information: "Regular expression to delete key (i.e. amino acids and
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45 nucleotides)"
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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 list: data [
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51 information: "Kinds of codon usage data. R* hypothesizes amino acids which
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52 are not present in the gene"
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53 values: "A0: Absolute amino acid frequency ('AA');
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54 A1: Relative amino acid frequency ('RAAU');
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55 C0: Absolute codon frequency ('AF');
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56 C1: Relative codon frequency in a complete sequence;
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57 C2: Relative codon frequency in each amino acid ('RF');
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58 C3: Relative synonymous codon usage ('RSCU') ;
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59 C4: Relative adaptiveness; i.e., ratio to maximum of minor codon
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60 ('W')
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61 C5: Maximum (1) or minor (0) codon;
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62 R0: Absolute codon frequency ('AF');
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63 R1: Relative codon frequency in a complete sequence;
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64 R2: Relative codon frequency in each amino acid ('RF');
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65 R3: Relative synonymous codon usage ('RSCU') ;
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66 R4: Relative adaptiveness; i.e., ratio to maximum of minor codon
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67 ('W')
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68 R5: Maximum (1) or minor (0) codon"
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69 default: "R0"
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70 ]
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71
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72 boolean: accid [
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73 information: "Include to use sequence accession ID as query"
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74 default: "N"
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75 ]
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76
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77 endsection: advanced
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78
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79 section: output [
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80 information: "Output section"
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81 type: "page"
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82 ]
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83
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84 outfile: outfile [
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85 parameter: "Y"
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86 information: "Codon usage output file"
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87 knowntype: "codon usage"
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88 relations: "EDAM_data:2865 Codon usage bias"
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89 ]
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90
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91 endsection: output
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