Lena Week 4

1. Modify the gene sequence string so that it highlights or “tags” the special sequences within this gene, as follows (ellipses indicate bases in the sequence; note the spaces before the start tag and after the end tag):
   • -35 and -10 box of the promoter
     • 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"
   • transcription start site
     • cat infA-E.coli-K12.txt | sed "2s/atg/<tss>&<\/tss> /1"
   • ribosome binding site
     • cat infA-E.coli-K12.txt | sed "s/gagg/ <rbs>&<\/rbs> /g"
   • start codon
     • cat infA-E.coli-K12.txt | sed "2s/atg/ <start_codon>&<\/start_codon> /g"
   • stop codon (*Note: not final answer)
     • cat infA-E.coli-K12.txt | sed "2s/t[ag][ag]/ <stop_codon>&<\/stop_codon> /2"
   • terminator
     • cat infA-E.coli-K12.txt | sed "s/aaaaggt...........gcctttt..../ <terminator>&<\/terminator> /g"
2. What is the exact mRNA sequence that is transcribed from this gene?
3. What is the amino acid sequence that is translated from this mRNA?

• All commands in one string

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> /1" | sed "s/t[ag][ag]/ <stop>&<\/stop> /3" | sed "s/.../ \n /3" | sed "s/aaaaggt...........gcctttt..../ <terminator>&<\/terminator> /g" | sed "2s/atg/<tss>&<\/tss> /1"

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