Difference between revisions of "Laurmagee: Week 4"

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(=Added Start Codon)
(Added Sections and Formatting)
Line 1: Line 1:
 
===Transcription and Translation “Taken to the Next Level”===
 
===Transcription and Translation “Taken to the Next Level”===
==-10 box==
+
==-10 box of the promoter==
 
#cat [file] | sed "s/[ct]at[at]at/ -10 box/g"
 
#cat [file] | sed "s/[ct]at[at]at/ -10 box/g"
 
#cat [file] | sed "s/[ct]at[at]at/ <minus10box>&<\/minus10box> /g"
 
#cat [file] | sed "s/[ct]at[at]at/ <minus10box>&<\/minus10box> /g"
  
==Added -35 box==
+
==Added -35 box of the promoter==
 
#cat [file] | sed "s/tt[gt]ac[at]/ -35 box/g"
 
#cat [file] | sed "s/tt[gt]ac[at]/ -35 box/g"
 
#cat [file] | sed "s/tt[gt]ac[at]/ <minus35box>&<\/minus35box> /g"
 
#cat [file] | sed "s/tt[gt]ac[at]/ <minus35box>&<\/minus35box> /g"
Line 13: Line 13:
 
==Added Ribosome Binding Site==
 
==Added Ribosome Binding Site==
 
#cat [file] | sed "s/gag/ <rbs>&<\/rbs> /g"  
 
#cat [file] | sed "s/gag/ <rbs>&<\/rbs> /g"  
#cat [file] | sed "s/gag/ <rbs>&<\/rbs> /g" | sed "s/atg/start/g"
+
#cat [file] | sed "s/gag/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>/&\n/g"
 +
#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==
 
==Added Start Codon==
#cat [file] | sed "s/gag/ <rbs>&<\/rbs> /g" | sed "s/<\/rbs>/&\n/g" | sed "2s/atg/ <start_codon>&<\/start_codon> /1"
+
#cat [file] | sed "2s/atg/ <start_codon>&<\/start_codon> /1"
 +
#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==
 +
#cat [file] |
 +
#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"
 +
 
 +
==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?
  
 
[[Category: Journal Entry]]
 
[[Category: Journal Entry]]
 +
[[User:Laurmagee|Laurmagee]] ([[User talk:Laurmagee|talk]]) 17:13, 19 September 2013 (PDT)

Revision as of 00:13, 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] |
  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"

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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