Class Notes 2

• Consensus Sequence: brackets [] will add an either/or search to the command line
  • e.g.: [ct]at[at]at will use either c or t in the first box, and a or t in the second box
    • would create the following
      • cataat
      • tataat
      • cattat
      • tattat

• other half of a hairpin aaaggt is gcctttt
  • look at it this way:

aaaaggt

ttttccg

Commands

• \/ goes to the end of a command

cat infA-E.coli-K12.txt | sed "s/[ct]at[at]at/ HEREcat infA-E.coli-K12.txt ! /g"

• What happened?
  • !! stands for the last command that you typed
  • Proper way how to type command:cat infA-E.coli-K12.txt | sed "s/[ct]at[at]at/ HERE\!\!\! /g"
    • Find the -10 box: cat infA-E.coli-K12.txt | sed "s/[ct]at[at]at/ -10 HERE\!\!\! /g" | sed "s/tt[gt]ac[at]/ -35 HEEERE\!\!\! /g"
      • To get the true answer, -10 and -35 must be 15 characters apart (use periods)

• cat infA-E.coli-K12.txt | sed "s/[ct]at[at]at/ <minus10box>&<\/minus10box> /g" | sed "s/tt[gt]ac[at]/ <minus35box>&<\/minus35box> /g"
  • proper way to type command to find all available -10 and -35 boxes

• cat infA-E.coli-K12.txt | sed "s/cat[at]at/ <minus10box>&<\/minus10box> /g" | sed "s/................. <\/minus10/<minus35box> &/g"
  • [character]{#} repeats a character # amount of times. Must use "sed -r" to activate the command.
    • cat infA-E.coli-K12.txt | sed -r "s/cat[at]at/ <minus10box>&<\/minus10box> /g" | sed "s/.{17} <\/minus10/<minus35box> &/g"

• cat infA-E.coli-K12.txt | sed "s/cat[at]at/ <minus10box>&<\/minus10box> /g" | sed -r "s/.{17} <\/minus10/<\/minus35box> &/g" | sed "s/tt[gt]ac[at]<\/minus35box>/ <minus35box>&/g"
  • CORRECT ONE TO USE

Finding GAGG

• cat infA-E.coli-K12.txt | sed "s/cat[at]at/ <minus10box>&<\/minus10box> /g" | sed -r "s/.{17} <\/minus10/<\/minus35box> &/g" | sed "s/tt[gt]ac[at]<\/minus35box>/ <minus35box>&/g" | sed "s/gagg/ <rbs>&<\/rbs> /g"

• cat infA-E.coli-K12.txt | sed "s/cat[at]at/ <minus10box>&<\/minus10box> /g" | sed -r "s/.{17} <\/minus10/<\/minus35box> &/g" | sed "s/tt[gt]ac[at]<\/minus35box>/ <minus35box>&/g" | sed "s/gagg/ <rbs>&<\/rbs> /g" | sed "s/atg/ HEEEERE /g"
  • Finds all ATG start sites, but doesn't indicate the one after the ribosome binding site

• cat infA-E.coli-K12.txt | sed "s/cat[at]at/ <minus10box>&<\/minus10box> /g" | sed -r "s/.{17} <\/minus10/<\/minus35box> &/g" | sed "s/tt[gt]ac[at]<\/minus35box>/ <minus35box>&/g" | sed "s/gagg/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>.&atg/ HEEEERE /g"
  • Still doesn't quite indicate the proper ATG

• cat infA-E.coli-K12.txt | sed "s/cat[at]at/ <minus10box>&<\/minus10box> /g" | sed -r "s/.{17} <\/minus10/<\/minus35box> &/g" | sed "s/tt[gt]ac[at]<\/minus35box>/ <minus35box>&/g" | sed "s/gagg/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>/&\n/g"

• cat infA-E.coli-K12.txt | sed "s/cat[at]at/ <minus10box>&<\/minus10box> /g" | sed -r "s/.{17} <\/minus10/<\/minus35box> &/g" | sed "s/tt[gt]ac[at]<\/minus35box>/ <minus35box>&/g" | sed "s/gagg/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>/&\n/g" | sed "2s/atg/ HEEEEERE /g"
  • cat infA-E.coli-K12.txt | sed "s/cat[at]at/ <minus10box>&<\/minus10box> /g" | sed -r "s/.{17} <\/minus10/<\/minus35box> &/g" | sed "s/tt[gt]ac[at]<\/minus35box>/ <minus35box>&/g" | sed "s/gagg/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>/&\n/g" | sed "2s/atg/ HEEEEERE /1"
    • replaced last g with 1 to look for a certain match

cat infA-E.coli-K12.txt | sed "s/cat[at]at/ <minus10box>&<\/minus10box> /g" | sed -r "s/.{17} <\/minus10/<\/minus35box> &/g" | sed "s/tt[gt]ac[at]<\/minus35box>/ <minus35box>&/g" | sed "s/gagg/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>/&\n/g" | sed "2s/atg/ <start_codon>&<\/start_codon> /g"