Mpetredi Week 3

Compliment of a Strand

cat infA-E.coli-K12.txt | sed "y/atcg/tagc/"

Reading Frames

Positive (Forward)

1. cat infA-E.coli-K12.txt | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed
2. cat infA-E.coli-K12.txt | sed "s/^.//g" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed
3. cat infA-E.coli-K12.txt | sed "s/^..//g" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed

Negative (Reverse)

1. cat infA-E.coli-K12.txt | sed "y/atcg/uagc/" | rev | sed "s/.../& /g" | sed -f genetic-code.sed
2. cat infA-E.coli-K12.txt | sed "y/atcg/uagc/" | sed "s^.//g" | rev | sed "s/.../& /g" | sed -f genetic-code.sed
3. cat infA-E.coli-K12.txt | sed "y/atcg/uagc/" | sed "s^..//g" | rev | sed "s/.../& /g" | sed -f genetic-code.sed

XMLPipeDB Match Practice

1. java -jar xmlpipedb-match-1.1.1.jar "GO:000916." < 493.P_falciparum.xml
   • There were 2 unique matches
   • Each unique match appears twice in the first line and once in the second line