Kevinmcgee Week 3

Genetic Code By Computer

Complementary Strand

seq_file | sed "y/actg/tagc/"

Reading Frame Codes

+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?

• 2 unique matches
• First match occurred twice, second match occured once.
• There appears to be multiple references to this in the doccument. It appears to be a specific alignment on a protein sequence of 493.P-Falciparum

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

• 2 Unique matches
• First match occurred 8238 times, second match occurred 1 time.
• When I typed in the command grep "\James.*\"", it told me that it was a persons name. By looking at the title and noticing the file is copyrighted, I believe that it is safe to assume that James K.D. is the name of an author of a scientific article.

1. 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 brought back 830,101 matches
• grep and wc gave me 502,401 lines, 502,401 words and 35671048 letters
• It makes sense that grep and wc had less matches because they cannot account for multiple matches on the same line.

Kevinmcgee (talk) 11:14, 12 September 2013 (PDT)