Dwilliams week 3

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.