Difference between revisions of "Bklein7 Week 3"

Revision as of 01:38, 17 September 2015

Complement of a Strand

Write a sequence of piped text processing commands that, when given a nucleotide sequence, returns its complementary strand. In other words, fill in the question marks:

   cat sequence_file | sed "y/atcg/tagc/"

Reading Frames

Write 6 sets of text processing commands that, when given a nucleotide sequence, returns the resulting amino acid sequence, one for each possible reading frame for the nucleotide sequence.

Outputs generated using ~dondi/xmlpipedb/data/prokaryote.txt:

• +1 Reading Frame

   cat sequence_file | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[atcg]//g" | sed "s/ //g"
   Output: STIFQ-VRWPKKTILNLKRCLIPCSAYNPAASSAGGIL

• +2 Reading Frame

   cat sequence_file | sed "s/t/u/g" | sed "s/^.//g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[atcg]//g" | sed "s/ //g"
   Output: LLYFNRYDGQRRQY-T-NVA-YHVPRITQPPVPLAAF-

• +3 Reading Frame

   cat sequence_file | sed "s/t/u/g" | sed "s/^..//g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[atcg]//g" | sed "s/ //g"
   Output: YYISIGTMAKEDNIELETLPNTMFRV-PSRQFRWRHFN

• -1 Reading Frame

   cat sequence_file | sed "y/atcg/tagc/" | sed "s/t/u/g" | rev | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[atcg]//g" |
   sed "s/ //g"
   Output: VKMPPAELAAGLYAEHGIRQRFKENIVFFGHRTY-NIV

• -2 Reading Frame

   cat sequence_file | sed "y/atcg/tagc/" | sed "s/t/u/g" | rev | sed "s/^.//g" | sed "s/.../& /g" | sed -f genetic-code.sed | 
   sed "s/[atcg]//g" | sed "s/ //g"
   Output: LKCRQRNWRLGYTRNMVLGNVSSSILSSLAIVPIEI--

• -3 Reading Frame

   cat sequence_file | sed "y/atcg/tagc/" | sed "s/t/u/g" | rev | sed "s/^..//g" | sed "s/.../& /g" | sed -f genetic-code.sed |
   sed "s/[atcg]//g" | sed "s/ //g"
   Output: -NAASGTGGWVIRGTWY-ATFQVQYCLLWPSYLLKYSR

Check Your Work

The ExPASy Translate Tool was used to confirm that the output sequences generated above were accurate translations. Below is the output generated by ExPASy for the same nucleotide sequence adapted from prokaryote.txt.

Media:ExPASy Prokaryote.txt Translation.png