Difference between revisions of "Laurmagee: Week 4"

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(Ribosome Binding Site)
(Last Addition RBS)
Line 15: Line 15:
 
*#cat [file] | sed "s/gag/ <rbs>&<\/rbs> /g"  
 
*#cat [file] | sed "s/gag/ <rbs>&<\/rbs> /g"  
 
*#cat [file] | sed "s/gag/ <rbs>&<\/rbs> /g" | sed "s/atg/start/g"
 
*#cat [file] | sed "s/gag/ <rbs>&<\/rbs> /g" | sed "s/atg/start/g"
*#cat [file] | sed "s/gag/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>/&\n/g" | sed "2s/atg/start/1"
+
*#cat [file] | sed "s/gag/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>/&\n/g" | sed "2s/atg/ <start_codon>&<\/start_codon> /1"

Revision as of 17:34, 17 September 2013

  • -10 box
    1. cat [file] | sed "s/[ct]at[at]at/ -10 box/g"
    2. cat [file] | sed "s/[ct]at[at]at/ <minus10box>&<\/minus10box> /g"
  • -35 box
    1. cat [file] | sed "s/tt[gt]ac[at]/ -35 box/g"
    2. cat [file] | sed "s/tt[gt]ac[at]/ <minus35box>&<\/minus35box> /g"
  • Together
    1. cat [file] | sed "s/[ct]at[at]at/ <minus10box>&<\/minus10box> /g" | sed "s/................. <minus10/ <\/minus35box> &/g"
    2. cat [file] | sed "s/[ct]at[at]at/ <minus10box>&<\/minus10box> /g" | sed -r "s/.{17} <minus10/ <\/minus35box> &/g"
    3. cat [file] | sed "s/[ct]at[at]at/ <minus10box>&<\/minus10box> /g" | sed -r "s/.{17} <minus10/ <\/minus35box> &/g" | sed "s/"s/tt[gt]ac[at]<\/minus35box>/ <minus35box>&/g"
  • Ribosome Binding Site
    1. cat [file] | sed "s/gag/ <rbs>&<\/rbs> /g"
    2. cat [file] | sed "s/gag/ <rbs>&<\/rbs> /g" | sed "s/atg/start/g"
    3. cat [file] | sed "s/gag/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>/&\n/g" | sed "2s/atg/ <start_codon>&<\/start_codon> /1"
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