Difference between revisions of "Malverso Week 3"

From LMU BioDB 2015
Jump to: navigation, search
(answered Complement of Strand.)
(answered Reading Frames for -1 strand.)
Line 6: Line 6:
 
  cat prokaryote.txt | sed "y/atgc/tacg/"  
 
  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
  
  
 
{{Template:Malverso}}
 
{{Template:Malverso}}

Revision as of 00:45, 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


Team Page

Heavy Metal HaterZ

Assignments

Individual Journal Entries

Shared Journal Entries

Retrieved from "https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?title=Malverso_Week_3&oldid=1506"