Lena Week 3
Genetic Code by Computer
Compliment of a Reading Strand
- sed "y/atcg/tagc/"
Reading Frames
- +1 seq_file | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
- +2 seq_file | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
- +3 seq_file | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
- -1 seq_file | sed "y/actg/tgac/" | rev | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
- -2 seq_file | sed "y/actg/tgac/" | rev | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
- -3 seq_file | sed "y/actg/tgac/" | rev | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
XMLPipeDB Match Practice
1.) What Match command tallies the occurrences of the pattern GO:000916. in the 493.P_falciparum.xml file?
- How many unique matches are there?
There are 2 unique matches.
- How many times does each unique match appear?
Twice for the one ending in 5 and once for the one ending in 8.
- What information do you think the pattern GO:000916. represents?
It represents a gene ontology term.
2. What Match command tallies the occurrences of the pattern \"James.*\" in the 493.P_falciparum.xml file?
- How many unique matches are there?
There are two unique matches.
- How many times does each unique match appear?
James k.d. appears 8238 times, james a.a appears once.
- What information do you think the pattern \"James.*\" represents?
Well the text says person name=James K.D., so I think I can safely say it represents a person. I don’t know who that person might be, maybe the person who created the file…
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.
- What answer does Match give you?
It says I there is one unique match.
- What answer does grep/wc give you?
Grep/wc gives me 502410 words.
- Do the answers make sense? Explain your response.
Yes. The reading says that Match can distinguish patterns better than grep and wc; match knows whether a pattern is unique or not while grep counts repeats.
- By Lena Hunt
