Difference between revisions of "Laurmagee: Week 4"

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(Added Stop Codon)
(Fixed Added Stop Codon)
Line 21: Line 21:
  
 
==Added Stop Codon==
 
==Added Stop Codon==
−
#cat [file] c
+
#cat [file] | sed "#s/tga/ <stop_codon>&<\/stop_codon>/#" | sed "#s/tag/ <stop_codon>&<\/stop_codon>/#" | sed "#s/taa/ <stop_codon>&<\/stop_codon>/#"
 
#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>/#"
 
#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.
 
  
 
==Transition Start Site==
 
==Transition Start Site==

Revision as of 01:13, 20 September 2013

Contents

Transcription and Translation “Taken to the Next Level”

-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] | sed "#s/tga/ <stop_codon>&<\/stop_codon>/#" | sed "#s/tag/ <stop_codon>&<\/stop_codon>/#" | sed "#s/taa/ <stop_codon>&<\/stop_codon>/#"
  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>/#"

Transition Start Site

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)

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