Kmeilak Week 3

Week 2 (corrected)

Kmeilak Week 2

Where's your stuff?

Link to html: [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

• +2 strand:

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

• +3 strand:

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

• -1 strand:

cat prokaryote.txt | sed "y/atcg/uagc/" | rev | sed "s/.../& /g" | sed -f genetic-code.sed

• -2 strand:

cat prokaryote.txt | sed "y/atcg/uagc/" | sed "s^.//g" | rev | sed "s/.../& /g" | sed -f genetic-code.sed

• -3 strand:

cat prokaryote.txt | sed "y/atcg/uagc/" | sed "s^..//g" | rev | sed "s/.../& /g" | sed -f genetic-code.sed

XMLPipeDB Match Practice

1. The Match command that tallies the occurrences of the pattern GO:000916. in the 493.P_falciparum.xml file is

• 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

• 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.