Difference between revisions of "KSherbina Week 3"
From LMU BioDB 2013
(Inputted response to first question in the XMLPipeDB Match Practice.) |
(→XMLPipeDB Match Practice: Inputted my response to the second question.) |
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#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. | #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. | ||
| − | # | + | #There are two unique matches: "james k.d." and "james a.a.". The pattern "james k.d." appears 8238 times while the pattern "james a.a." appears only once in the file. These patterns probably designate the names of the scientists who determined the genetic sequence of ''P. falciparum''. |
Revision as of 06:11, 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.
- There are two unique matches: "james k.d." and "james a.a.". The pattern "james k.d." appears 8238 times while the pattern "james a.a." appears only once in the file. These patterns probably designate the names of the scientists who determined the genetic sequence of P. falciparum.
