Difference between revisions of "KSherbina Week 3"
From LMU BioDB 2013
(→Reading Frames: Corrected commands to translate -1, -2, and -3 reading frames.) |
(Inputted response to first question in the XMLPipeDB Match Practice.) |
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*the -1 reading frame: | *the -1 reading frame: | ||
cat prokaryote.txt | sed "y/atcg/tagc/" | rev | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | cat prokaryote.txt | sed "y/atcg/tagc/" | rev | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed | ||
| + | |||
| + | ===XMLPipeDB Match Practice=== | ||
| + | |||
| + | #There are two unique matches: go:0009165 and go:0009165. The pattern go:009165 appears twice and the pattern go:009165 appears once in the file. These patterns represent a gene ontology term, which describes what biological function the product of a gene is involved in. | ||
| + | # | ||
Revision as of 06:05, 13 September 2013
| Assignment Description | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 | Week 12 | Week 13 | Week 15 |
| Class Journal | Week 1 | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | |||||
| Individual Journal | Week 2 | Week 3 | Week 4 | Week 5 | Week 6 | Week 7 | Week 8 | Week 9 | Week 10 | Week 11 |
| Other | Week 5: Database Wiki |
| Final Project | Team H(oo)KD Project Page | Journal Club Presentation | Project Individual Journal |
Contents |
The Genetic Code, by Computer
Complement of a Strand
To find the complementary strand of the sequence in the file prokaryote.txt, the following sequence of piped text was executed
cat prokaryote.txt | sed "y/atcg/tagc/"
Reading Frames
The following piped sequence of text was invoked to determine the sequence of amino acids encoded by
- the +1 reading frame:
cat prokaryote.txt | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
- the +2 reading frame:
cat prokaryote.txt | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
- the +3 reading frame:
cat prokaryote.txt | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
- the -1 reading frame:
cat prokaryote.txt | sed "y/atcg/tagc/" | rev | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
- the -2 reading frame:
cat prokaryote.txt | sed "y/atcg/tagc/" | rev | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
- the -1 reading frame:
cat prokaryote.txt | sed "y/atcg/tagc/" | rev | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
XMLPipeDB Match Practice
- There are two unique matches: go:0009165 and go:0009165. The pattern go:009165 appears twice and the pattern go:009165 appears once in the file. These patterns represent a gene ontology term, which describes what biological function the product of a gene is involved in.
