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/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/tt[gt]ac[at]<\/minus35box>/ <minus35box>&/g" | sed "s/gagg/ <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/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"

Added Stop Codon

1. cat [file] | sed "s/<\/start_codon>/&\n/g" | sed "s/.../&/g" | sed "4s/tag/ <stop_codon>&<\/stop_codon>/1"
2. cat [file] | sed "s/[ct]at[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/<\/start_codon>/&\n/g" | sed "s/.../& /g" | sed "4s/tag/ <stop_codon>&<\/stop_codon>/1" | sed "4s/tga/ <stop_codon>&<\/stop_codon>/1" | sed "4s/taa/ <stop_codon>&<\/stop_codon>/1"

Transition Start Site

1. cat [file] | sed "s/.{12} <minus10/ <tss>&<\/tss>/g"
2. cat [file] | sed "s/[ct]at[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/<\/start_codon>/&\n/g" | sed "s/.../& /g" | sed "4s/tag/ <stop_codon>&<\/stop_codon>/1" | sed "4s/tga/ <stop_codon>&<\/stop_codon>/1" | sed "4s/taa/ <stop_codon>&<\/stop_codon>/1" | sed -r "s/.{12} <minus10/ <tss>&<\/tss>/g"

Terminator

1. cat [file] | sed "s/aaaaggt .{4}/ <terminator>&<\/terminator>/g"
   1. cat [file] | sed "s/[ct]at[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/<\/start_codon>/&\n/g" | sed "s/.../& /g" | sed "4s/tag/ <stop_codon>&<\/stop_codon>/1" | sed "4s/tga/ <stop_codon>&<\/stop_codon>/1" | sed "4s/taa/ <stop_codon>&<\/stop_codon>/1" | sed -r "s/.{12} <minus10/ <tss>&<\/tss>/g" | sed -r "s/aaaaggt .{4}/ <terminator>&<\/terminator>/g"

Transcribed mRNA sequence

• augugccgaaccuguuuguugcgauuuagcgcgcaaaucuuuacuuauuuacagaacuucggcauuaucuugccgguucaaauuacgguagugauaccccagaggauuagauggcc

aaagaagacaauauugaaaugcaagguaccguucuugaaacguugccuaauaccauguuccgcguag

Translated amino acid sequence

• Met C R T C L L R F S A Q I F T Y L Q N F G I I L P V Q I T V V I P Q R I R W P K K T I L K C K V P F L K R C L I P C S A Stop

• Laurmagee (talk) 17:13, 19 September 2013 (PDT)