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1 application: gdinuc [
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2 documentation: "Calculates dinucleotide usage "
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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:0377 Sequence composition calculation
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7 (nucleic acid)"
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8 ]
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9
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10 section: input [
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11 information: "Input section"
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12 type: "page"
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13 ]
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14
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15 seqall: sequence [
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16 parameter: "Y"
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17 type: "nucleotide"
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18 features: "Y"
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19 relations: "EDAM_data:0849 Sequence record"
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20 ]
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21
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22 endsection: input
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23
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24 section: advanced [
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25 information: "Advanced section"
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26 type: "page"
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27 ]
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28
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29 boolean: translate [
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30 information: "Include when translates using standard codon table"
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31 default: "N"
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32 ]
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33
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34 list: position [
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35 information: "Codon position or reading frame"
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36 values: "all:Assess all codon positions;
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37 12:Assess the reading frame 1-2;
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38 23:Assess the reading frame 2-3;
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39 31:Assess the reading frame 3-1"
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40 default: "all"
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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 nucleotides)"
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45 knowntype: "regular expression"
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46 default: "[^ACDEFGHIKLMNPQRSTVWYacgtU]"
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47 ]
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48
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49 boolean: accid [
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50 information: "Include to use sequence accession ID as query"
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51 default: "N"
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52 ]
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53
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54 endsection: advanced
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55
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56 section: output [
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57 information: "Output section"
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58 type: "page"
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59 ]
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60
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61 outfile: outfile [
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62 parameter: "Y"
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63 information: "Program compseq output file"
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64 knowntype: "compseq output"
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65 relations: "EDAM_data:3086 Nucleic acid sequence composition"
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66 ]
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67
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68 endsection: output
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