Stephen Louie Week 3

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Complement of a Strand

The command I used to get the complement strand was:

cat prokaryote.txt | sed "y/atcg/tagc/"

Reading Frames

The six sets of text proccessing commands I used were:

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

Corrections:

cat prokaryote.txt | sed "y/atcg/tagc/" | rev | 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

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 appears 2 times. GO:0009168 appears 1 time. I believe GO:000916 is a specific strain of bacterium
2. There are two unique matches. "James K.D." appears 8238 times. "James A.A." appears once. \"James.*\ probably represents the name of an author.
3. Match gave 165 occurrences. grep/wc gave 162 occurrences. Theses answers make sense due to the unique ways in which Match and grep/wc count for their occurrences. Match reads the entire file as a single line while grep/wc breaks and scans the file in chunks. The reasons grep/wc has less occurrences is because when the file is split up into chunks it can split a certain match in two pieces resulting in a lost match. Since Match looks at the file in a single line, none of the matches are at risk of being split apart. Match found 830,101 occurrences. grep/wc gave 502,410 occurrences. Match reads the entire file as a single line while grep/wc breaks and scans the file in chunks. The reasons grep/wc has less occurrences is because when the file is split up into chunks it can split a certain match in two pieces resulting in a lost match. Since Match looks at the file in a single line, none of the matches are at risk of being split apart.

Slouie (talk) 11:18, 17 September 2013 (PDT)