Dwilliams week 3
From LMU BioDB 2013
Contents |
Genetic Code By Computer
Complement of Strand
cat prokaryote.txt | sed "y/atcg/tagc/"
Translation of the Genetic Code
+1 Frame
cat prokaryote.txt | sed "s/t/u/g" | sed "s/.../& /" | sed -f genetic-code.sed
Result:
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 Frame
cat prokaryote.txt | sed "s/t/u/g" | sed "s/^.//g" | sed "s/.../& /g" | sed -f genetic-code.sed
Result:
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 Frame
cat prokaryote.txt | sed "s/t/u/g" | sed "s/^..//g" | sed "s/.../& /g" | sed -f genetic-code.sed
Result:
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 Frame
cat prokaryote.txt | rev| sed "y/atcg/uagc/" | sed "s/.../& /g" | sed -f genetic-code.sed
Result:
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 Frame
cat prokaryote.txt | rev| sed "y/atcg/uagc/" | sed "s/^.//g" | sed "s/.../& /g" | sed -f genetic-code.sed
Result:
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 Frame
cat prokaryote.txt | rev| sed "y/atcg/uagc/" | sed "s/^.//g" | sed "s/.../& /g" | sed -f genetic-code.sed
Result:
- 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 Practice
1.
- Two unique matches.
- First match occurs twice, second match occurs once.
- I would assume that "GO:000916" probably refers to a specific line of code.
2.
- Two unique matches.
- James a.a. appears once; James k.d. appears 8,238 times. I would assume that james refers to/identifies an author.
3.
- 830,101
- 502,410
- The answers make sense because the occurence of ATG will only be counted once per line, regardless of whether or not their are multiple sequences of ATG in that same line.