Kmeilak Week 3
From LMU BioDB 2013
Contents |
Week 2 (corrected)
Where's your stuff?
Was unable to successfully upload .txt or .html files. However, I was able to successfully make an html file that was opened by a web browser and is saved on my computer at this location [file:///C:/Users/Kevin/Desktop/Week%203%20homework.html link to Kevin's html]
The Genetic Code by Computer
Complement of a Strand
The way to return a strand's complement is by inputting the following
cat prokaryote.txt | sed "y/atcg/tagc/"
Reading Frames
- +1 strand:
cat prokaryote.txt | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed
translates as
S T I F Q - V R W P K K T I L N L K R C L I P C S A Y N P A A S S A G G I L
- +2 strand:
cat prokaryote.txt | sed "s/^.//g" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed
translates as
L L Y F N R Y D G Q R R Q Y - T - N V A - Y H V P R I T Q P P V P L A A F -
- +3 strand:
cat prokaryote.txt | sed "s/^..//g" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed
translates as
Y Y I S I G T M A K E D N I E L E T L P N T M F R V - P S R Q F R W R H F N
- -1 strand:
cat prokaryote.txt | sed "y/atcg/uagc/" | rev | sed "s/.../& /g" | sed -f genetic-code.sed
translates as
V K M P P A E L A A G L Y A E H G I R Q R F K F N I V F F G H R T Y - N I V
- -2 strand:
cat prokaryote.txt | sed "y/atcg/uagc/" | sed "s^.//g" | rev | sed "s/.../& /g" | sed -f genetic-code.sed
translates as
L K C R Q R N W R L G Y T R N M V L G N V S S S I L S S L A I V P I E I - -
- -3 strand:
cat prokaryote.txt | sed "y/atcg/uagc/" | sed "s^..//g" | rev | sed "s/.../& /g" | sed -f genetic-code.sed
translates as
- N A A S G T G G W V I R G T W Y - A T F Q V Q Y C L L W P S Y L L K Y S R
XMLPipeDB Match Practice
1. The Match command that tallies the occurrences of the pattern GO:000916. in the 493.P_falciparum.xml file sends the web server to a line of code.
- There are 2 unique matches
- the first unique match (go:0009165) appears twice, and the second unique match (go:0009168) appears once
- The pattern GO:000916. represents
2. The Match command that tallies the occurrences of the pattern \"James.*\" in the 493.P_falciparum.xml file is an author.
- There are 2 unique matches
- The first unique match ("james k.d.") appears 8238 times and the second unique match ("james a.a.") appears 1 time
- The pattern \"James.*\" represents
3. ATG Results
- The answer Match gave me was that ATG appeared 830101 times
- grep/wc said that ATG appeared 502410 times
- Yes, these responses do make sense. Match looks only for the pattern ATG, but grep/wc searches for the number of lines of code where the sequence appears, which means any lines with multiple appearances of ATG are counted as a single result.
- Main Page
- Kevin's User Page
- Week 1
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- Class Journal Week 1
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- Class Journal Week 15
- Kmeilak Week 2
- Kmeilak Week 3
- Kmeilak Week 4
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- Kmeilak Week 6
- Kmeilak Week 7
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- Kmeilak Week 12
- Kmeilak Week 13
- Kmeilak Week 14
- Kmeilak Week 15
