Emilysimso Week 4

Question 1

• Used grep "[ct]at[at]at" infA-E.coli-K12.txt to highlight the -10box
• Used grep "tt[gt]ac[at]" infA-E.coli-K12.txt to highlight the -35 box
• Used sed "s/cattat/<minus10box>&<\/minus10box>/g" infA-E.coli-K12.txt | sed "s/tttact/<minus35box>&<\/minus35box>/g" to add the labels to the -35box and -10box

• Added sed -r "s/<\/minus10box>.{11}/<tss>&<\/tss>/g"
  • This did not work because the <tss> label got added before the </minus10box>

• Used sed -r "s/<\/minus10box>.{5}/&<\/tss>/g" | sed "s/<\/tss>/<tss>c&/g" to add the tss site markers

• Added grep "gagg" to find the rbs
• Added sed "s/gagg/<rbs>&<\/rbs>/g" around the gagg to mark the rbs

• Used grep "atg" to find possible start codons
• Added sed -r "s/<\/rbs>.{8}/&<\/startcodon>/g" | sed "s/<\/startcodon>/<startcodon>atg&/g" to mark the start codon (atg)

sed "s/cattat/<minus10box>&<\/minus10box>/g" infA-E.coli-K12.txt | sed "s/tttact/<minus35box>&<\/minus35box>/g" | sed -r "s/<\/minus10box>.{5}/&<\/tss>/g" | sed "s/<\/tss>/<tss>c&/g" | sed "s/gagg/<rbs>&<\/rbs>/g" | sed -r "s/<\/rbs>.{8}/&<\/startcodon>/g" | sed "s/<\/startcodon>/<startcodon>atg&/g"

• Possible stop codons - taa, tag, or tga