Vkuehn Week 3

Individual Journal Assignment Week 3

Complement of a Strand

cat sequence_file | grep "aggta" prokaryote.txt | sed "s/aggta/tccat/g" prokaryote.txt

Reading Frames:

+1 Reading Frame:

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

+2 Reading Frame:

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

+3 Reading Frame:

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

Reverse Reading Frames:

-1 Reading Frame:

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

-2 Reading Frame:

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

-3 REading Frame:

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

XMLPipeDB Match Practice:

What Match command tallies the occurrences of the pattern GO:000916. in the 493.P_falciparum.xml file?

• 2 unique matches
• One match appears once, and the other appears twice.
• I think this represents some kind of a protein marker or specific sequence.

What Match command tallies the occurrences of the pattern \"James.*\" in the 493.P_falciparum.xml file?

• dfajsdfao
• dsfasdf
• This information represents the authors who found certain proteins gene sequences.

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.

Viktoria Kuehn

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