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1 application: gbasecounter [
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2 documentation: "Creates a position weight matrix of oligomers around start
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3 codon"
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4 groups: "Nucleic:Composition"
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5 embassy: "gembassy"
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6 relations: "EDAM_topic:0157 Sequence composition analysis"
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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 selection: position [
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31 information: "Either 'start' (around start codon) or 'end'
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32 (around stop codon) to create the PWM"
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33 values: "start;end"
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34 default: "start"
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35 ]
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36
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37 integer: patlen [
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38 information: "Length of oligomer to count"
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39 default: "3"
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40 ]
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41
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42 integer: upstream [
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43 information: "Length upstream of specified position to create PWM"
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44 default: "30"
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45 ]
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46
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47 integer: downstream [
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48 information: "Length downstream of specified position to create PWM"
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49 default: "30"
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50 ]
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51
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52 boolean: accid [
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53 information: "Include to use sequence accession ID as query"
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54 default: "N"
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55 ]
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56
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57 endsection: advanced
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58
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59 section: output [
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60 information: "Output section"
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61 type: "page"
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62 ]
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63
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64 outfile: outfile [
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65 parameter: "Y"
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66 information: "Weight matrix output file"
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67 knowntype: "matrix"
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68 relations: "EDAM_data:1362 Position weight matrix"
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69 ]
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70
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71 endsection: output
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