KSherbina Week 3

Katrina Sherbina

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Assignment Description

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Class Journal

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Week 5: Database Wiki

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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

1. 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.
2. 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.
3. According to Match, the pattern ATG appears 165 times in the file. However, according to grep, the pattern ATG appears 162 times. The discrepancy makes sense considering that grep searches for patterns one line at a time while Match searches all of the text continuously for a specific pattern. There may have been three ATG patterns that were broken up between two consecutive lines. Thus, Match was able to find them, whereas grep was not.

Ksherbina (talk) 23:17, 12 September 2013 (PDT)