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 are 2 unique matches.
   • Each unique match appears twice in the first line and once in the second line.
2. java -jar xmlpipedb-match-1.1.1.jar "\"James.*\"" < 493.P_falciparum.xml
   • There are 2 unique matches.
   • The first line (james k.d.) has 8238 matches, and the second line james a.a. has 1 match.
   • "James" may refer to the person who sequenced all or a portion of falciparum.
3. Use Match to count the occurrences of the pattern ATG in the hs_ref_GRCh37_chr19.fa file (this may take a while). Then, use grep and wc to do the same thing.
   • Match ATG results in 1 unique match appearing 830101 times
   • grep and wc result in 502410 lines, 502410 words, and 35671048 characters
   • These answers make sense because Match is only looking for a specific instance when ATG appears, which would make its value lower than the grep | wc combo. grep | wc cannot differentiate specific pieces of text and yields any occurrence when the pattern ATG comes up.

Mpetredi (talk) 21:53, 12 September 2013 (PDT)Mitchell Petredis