Difference between revisions of "Gleis Week 3"

Latest revision as of 05:20, 17 September 2013

[edit] XMLPIPEDB MATCH

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

• Two unique matches
• First unique match occurred twice. Second match occurred once
• GO:000916 possibly represents a sequence identification number for a portion of a protein sequence.

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

• Two unique matches
• The first unique match occurred 8283 times and the second unique match occurred once.
• \"James.*\" likely refers to the last name of an author in a journal article.

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.

• 830101
• 502410
• The answers make sense because grep wc will only count the occurrence of ATG once per line even if ATG occurs more than once.

[edit] The Genetic Code, By Computer

[edit] Complement of a Strand

cat sequence_file | sed "y/atgc/tacg/"

[edit] Reading Frames

+1 cat sequence_file | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed

+2 cat sequence_file | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed

+3 cat sequence_file | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed

-1 cat sequence_file | sed "y/atgc/tacg/" | rev | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed

-2 cat sequence_file | sed "y/atgc/tacg/" | rev | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed

-3 cat sequence_file | sed "y/atgc/tacg/" | rev | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed

Gleis (talk) 22:18, 16 September 2013 (PDT)