Malverso Week 3
Contents
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
I checked my work using the ExPASy Translate Tool.
+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/[augc]//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-
+3
All I did was add a "." to the sed command to delete the front two letters instead of just one:
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 proved to be successful:
YYISIGTMAKEDNIELETLPNTMFRV-PSRQFRWRHFN
-1
At first I thought all I had to do was add rev prokaryote.txt to the beginning of the previous three. I was mistaken. I realized that I needed to first change the bases to their complements, which I did with the code I wrote for the first homework question. My code:
cat prokaryote.txt | rev prokaryote.txt | sed “y/agtc/tacg/” | sed "s/.../& /g" | sed "y/t/u/" | sed -f genetic-code.sed | sed "s/[aguc]//g" | sed "s/ //g"
which produced:
VKMPPAELAAGLYAEHGIRQRFKFNIVFFGHRTY-NIV
-2
Then I just took off the first character of the line, and used the code as follows:
cat prokaryote.txt | rev prokaryote.txt | sed "s/^.//g" | sed "y/agtc/tcag/" | sed "s/.../& /g" | sed "y/t/u/" | sed -f genetic-code.sed | sed "s/[aguc]//g" | sed "s/ //g"
This was the result:
LKCRQRNWRLGYTRNMVLGNVSSSILSSLAIVPIEI--
-3
And finally, I took off two characters from the beginning of the line instead of one:
cat prokaryote.txt | rev prokaryote.txt | sed "s/^..//g" | sed "y/agtc/tcag/" | sed "s/.../& /g" | sed "y/t/u/" | sed -f genetic-code.sed | sed "s/[aguc]//g" | sed "s/ //g"
Which produced:
-NAASGTGGWVIRGTWY-ATFQVQYCLLWPSYLLKYSR
XMLPipeDB Match Practice
I used putty.exe to access the match program, and used the Using the XMLPipeDB Match Utility page as a resource.
#1
Here is the Match command:
java -jar xmlpipedb-match-1.1.1.jar "GO:000[567]" < 493.P_falciparum.xml
- There are 3 unique matches.
- Match appearances:
- go:0007: 113
- go:0006: 1100
- go:0005: 1371
#2
I used the command:
grep “GO:000[567]” 493.P_falciparum.xml
This gave me a list of all the occurrences of the pattern. I can infer that this pattern represents the database location numbers. An example of the pattern in a line of code is:
<dbReference type="GO" id="GO:0005875">
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