Vpachec3 Week 3
Contents
The Genetic Code, by Computer
cat prokaryote.txt | see "y/atcg/tagc/"
Reading Frames
+1
cat prokaryote.txt | sed "s/..$//g" | sed "y/t/u/" | sed "s/.../& /g" | sed -f genetic-code.sed
S T I F Q - V R W P K K T I L N L K R C L I P C S A Y N P A A S S A G G I L
+2
cat prokaryote.txt | sed "s/^.//g" | sed "s/.$//g" | sed "y/t/u" | sed "s/.../& /g" | sed -f genetic-code.sed
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
cat prokaryote.txt | sed "s/^..//g" | sed "y/t/u/" | sed "s/.../& /g" | sed -f genetic-code.sed
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
cat prokaryote.txt | sed "y/tagc/aucg/" | rev | sed "s/.../& /g" | sed "s/..$//g" | sed -f genetic-code.sed
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
cat prokaryote.txt | sed "y/tagc/aucg" | rev | sed "s/^..//g" | sed "s/.../& /g" | sed -f genetic-code.sed
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
cat prokaryote.txt | sed "y/tagc/aucg/" | rev | sed "s/^..//g" | sed "s/.../& /g" | sed -f genetic-code.sed
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
What Match command tallies the occurrences of the pattern GO:000[567] in the 493.P_falciparum.xml file? How many unique matches are there? How many times does each unique match appear?
Try to find one such occurrence “in situ” within that file. Look at the neighboring content around that occurrence.
Describe how you did this.
Based on where you find this occurrence, what kind of information does this pattern represent?
What Match command tallies the occurrences of the pattern \"Yu.*\" in the 493.P_falciparum.xml file?
How many unique matches are there?
How many times does each unique match appear?
What information do you think this pattern represents?
Use Match to count the occurrences of the pattern ATG in the hs_ref_GRCh37_chr19.fa file (this may take a while). Then, use grep and wc to do the same thing.
What answer does Match give you?
What answer does grep + wc give you?
Explain why the counts are different. (Hint: Make sure you understand what exactly is being counted by each approach.)
