Difference between revisions of "Malverso Week 3"

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(answered Reading Frames for -1 strand.)
(answered reading frames for -2 strand.)
Line 16: Line 16:
 
which had the output:
 
which had the output:
 
  STIFQ-VRWPKKTILNLKRCLIPCSAYNPAASSAGGIL
 
  STIFQ-VRWPKKTILNLKRCLIPCSAYNPAASSAGGIL
 +
 +
====-2====
 +
For this strand, the only change I had to make in my code was to get rid of the very first character of prokaryote.txt. At first, I added the command sed "s/^[agtc]//g", but realized that it also worked to use sed "s/^.//g". I chose the second choice which looked like:
 +
cat prokaryote.txt | sed "s/^.//g" | sed "s/.../& /g" | sed "y/t/u/" | sed -f genetic-code.sed | sed "s/[augc]//g" | sed "s/ //g"
 +
which had the output:
 +
LLYFNRYDGQRRQY-T-NVA-YHVPRITQPPVPLAAF-
 +
  
  
 
{{Template:Malverso}}
 
{{Template:Malverso}}

Revision as of 00:50, 22 September 2015

The Genetic Code, By Computer

I used putty.exe and logged in to my account on my.cs.lmu.edu in order to access prokaryote.txt.

Complement of a Strand

At first, I tried using the command cat prokaryote.txt | sed “s/atcg/tagc/g”, which was incorrect. I revisited my notes to see that it is actually: 

cat prokaryote.txt | sed "y/atgc/tacg/"

Reading Frames

-1

Using prokaryote.txt again, I used sed “y/t/u/” to replace all the t's with u's. I then re-read Introduction to the Command Line to find that sed –f <file with rules> is the technique I should use to use to harness the helpfullness of the genetic_code.sed file.

I tried cat prokaryote.txt | sed “y/t/u/” | sed –f genetic-code.sed, but when I checked that answer on the ExPASy Translate Tool it was wrong. Then I tried adding a space between each set of three letters with sed “s/…/& /g” which produced the correct answer but with some left over bases on the end.I added sed “s/[augc]//” to get rid of the left over bases, and then sed "s/ //g" to get rid of the spaces between the letters. This looked like: 

cat prokaryote.txt | sed "s/.../& /g" | sed "y/t/u/" | sed -f genetic-code.sed | sed "s/[atgc]//g" | sed "s/ //g"

which had the output: 

STIFQ-VRWPKKTILNLKRCLIPCSAYNPAASSAGGIL

-2

For this strand, the only change I had to make in my code was to get rid of the very first character of prokaryote.txt. At first, I added the command sed "s/^[agtc]//g", but realized that it also worked to use sed "s/^.//g". I chose the second choice which looked like: 

cat prokaryote.txt | sed "s/^.//g" | sed "s/.../& /g" | sed "y/t/u/" | sed -f genetic-code.sed | sed "s/[augc]//g" | sed "s/ //g"

which had the output: 

LLYFNRYDGQRRQY-T-NVA-YHVPRITQPPVPLAAF-



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