Bklein7 Week 3

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

Fortunately, online tools are available for checking your work; we recommend the ExPASy Translate Tool, sponsored by the same people who run SwissProt. You’re free to use this tool to see if your text processing commands produce the same results.