Difference between revisions of "Bklein7 Week 3"

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(Outlined the questions and supplied initial answers)
(Added command sequences for negative reading frames and their outputs)
Line 21: Line 21:
 
     Output: YYISIGTMAKEDNIELETLPNTMFRV-PSRQFRWRHFN
 
     Output: YYISIGTMAKEDNIELETLPNTMFRV-PSRQFRWRHFN
 
*'''-1 Reading Frame'''
 
*'''-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'''
 
*'''-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'''
 
*'''-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 |
−
* '''Hint 1:''' The 6 sets of commands are very similar to each other.
+
    sed "s/[atcg]//g" | sed "s/ //g"
−
* '''Hint 2:''' Under the ''~dondi/xmlpipedb/data'' directory in the Keck lab, you will find a file called ''genetic-code.sed''.  To save you some typing, this file has already been prepared with the correct sequence of '''sed''' commands for converting any base triplets into the corresponding amino acid.  For example, this line in that file: <pre>s/ugc/C/g</pre> ...corresponds to a uracil-guanine-cytosine sequence transcribing to the cysteine amino acid (C).  The trick is to figure out how to use this file to your advantage, in the commands that you'll be forming.
+
    Output: -NAASGTGGWVIRGTWY-ATFQVQYCLLWPSYLLKYSR
  
 
== Check Your Work ==
 
== 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.
 
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.

Revision as of 01:10, 16 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

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.

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