Difference between revisions of "Laurmagee: Week 4"

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"