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1 application: gbasezvalue [
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2 documentation: "Extracts conserved oligomers per position using Z-score"
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3 groups: "Nucleic:Composition"
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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 integer: limit [
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30 information: "Rank threshold for showing the conserved oligomer"
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31 default: "5"
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32 ]
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33
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34 selection: position [
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35 information: "Either 'start' (around start codon) or 'end'
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36 (around stop codon) to create the PWM"
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37 values: "start;end"
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38 default: "start"
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39 ]
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40
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41 integer: patlen [
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42 information: "Length of oligomer to count"
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43 default: "3"
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44 ]
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45
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46 integer: upstream [
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47 information: "Length upstream of specified position to create PWM"
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48 default: "30"
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49 ]
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50
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51 integer: downstream [
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52 information: "Length downstream of specified position to create PWM"
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53 default: "30"
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54 ]
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55
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56 boolean: accid [
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57 information: "Include to use sequence accession ID as query"
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58 default: "N"
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59 ]
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60
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61 endsection: advanced
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62
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63 section: output [
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64 information: "Output section"
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65 type: "page"
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66 ]
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67
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68 outfile: outfile [
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69 parameter: "Y"
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70 information: "Program compseq output file (optional)"
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71 knowntype: "compseq output"
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72 relations: "EDAM_data:3086 Nucleic acid sequence composition"
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73 ]
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74
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75 endsection: output
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