Taur.vil Week 3

Week 3 Individual Journal

Week 2 Correction

None were needed

Genetic Code by Computer

Complement of a strand

cat prokaryote.txt | sed "y/atcg/tagc/"

Translating the Genetic Code

+1 Frame

cat prokaryote.txt | sed "s/t/u/g" | sed "s/.../& /" | sed -f genetic-code.sed

Produces

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

Produces

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

Produces

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

Produces

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

Produces

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

Produces

- 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. There are two unique matches: go:0009165 which appears twice and go:0009168 which appears once. I believe that the go:000916. represents an instruction that refers the web server to a particular line of code.

java -jar xmlpipedb-match-1.1.1.jar "GO:000916." <493.P_falciparum.xml

1. Once again, there are two unique matches: james a.a. which appears once and james k.d. which appears 8,238 times. I believe the james information identifies an author.

java -jar xmlpipedb-match-1.1.1.jar "James.*" <493.P_falciparum.xml

1. Match found 830,101 occurances of ATG in the code while grep/wc found 502,410. These values are different because Match counts each time the code appears while grep only counts the number of lines containing ATG (which appears multiple times in the same line).

 java -jar xmlpipedb-match-1.1.1.jar "ATG" <hs_ref_GRCh37_chr19.fa

 grep "ATG" hs_ref_GRCh37_chr19.fa | wc

By Tauras Vilgalys

As part of Biological Databases

Please Remember the Harassing of Deities is Strictly Prohibited

Never Forget Samson