Difference between revisions of "Kmeilak Week 3"
From LMU BioDB 2013
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===Reading Frames=== | ===Reading Frames=== | ||
| − | *+1 strand: cat prokaryote.txt | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | + | *+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== | ==XMLPipeDB Match Practice== | ||
Revision as of 04:11, 13 September 2013
Contents |
Week 2 (corrected)
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.
