Laurmagee: Week 4

-10 box of the promoter

1. cat [file] | sed "s/[ct]at[at]at/ -10 box/g"
2. cat [file] | sed "s/[ct]at[at]at/ <minus10box>&<\/minus10box> /g"

Added -35 box of the promoter

1. cat [file] | sed "s/tt[gt]ac[at]/ -35 box/g"
2. cat [file] | sed "s/tt[gt]ac[at]/ <minus35box>&<\/minus35box> /g"
3. cat [file] | sed "s/[ct]at[at]at/ <minus10box>&<\/minus10box> /g" | sed "s/................. <minus10/ <\/minus35box> &/g"
4. cat [file] | sed "s/[ct]at[at]at/ <minus10box>&<\/minus10box> /g" | sed -r "s/.{17} <minus10/ <\/minus35box> &/g"
5. 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"

Added Ribosome Binding Site

1. cat [file] | sed "s/gag/ <rbs>&<\/rbs> /g"
2. cat [file] | sed "s/gag/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>/&\n/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" | sed "s/gag/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>/&\n/g"

Added Start Codon

1. cat [file] | sed "2s/atg/ <start_codon>&<\/start_codon> /1"
2. 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" | sed "s/gag/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>/&\n/g" | sed "2s/atg/ <start_codon>&<\/start_codon> /1"

Added Stop Codon

1. cat [file] c
2. 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" | sed "s/gag/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>/&\n/g" | sed "2s/atg/ <start_codon>&<\/start_codon> /1" | sed "#s/tga/ <stop_codon>&<\/stop_codon>/#" | sed "#s/tag/ <stop_codon>&<\/stop_codon>/#" | sed "#s/taa/ <stop_codon>&<\/stop_codon>/#"

The transcription start site is located at the 12th nucleotide after the first nucleotide of the -10 box. A consensus sequence for the ribosome binding site is gagg. The first half of the terminator “hairpin” is aaaaggt, where the u in the mRNA binds with a g instead of the usual a. The terminator includes 4 more nucleotides after the hairpin completes.

Terminator

What is the exact mRNA sequence that is transcribed from this gene? What is the amino acid sequence that is translated from this mRNA?Laurmagee (talk) 17:13, 19 September 2013 (PDT)