Difference between revisions of "HDelgadi Week 3"

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(6 Different Reading Frames)
(Updating answers to last set of questions)
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This pattern can represent the different labeled proteins.
 
This pattern can represent the different labeled proteins.
  
*What answer does Match give you?
+
*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. What answer does Match give you?
 
+
  
 +
Match gives me 830101 for the occurrences of the pattern ATG in the file.
  
 
*What answer does grep/wc give you?
 
*What answer does grep/wc give you?
 +
 +
Grep/wc gave me 502410 (lines), 502410 (words), and 35671048 (characters).
  
 
*Do the answers make sense? Explain your response.
 
*Do the answers make sense? Explain your response.
 +
 +
The answers for Match and grep/wc make sense because grep/wc gives us the number of occurrences in a line and counts them as one even if there's two combined, so it is expected to see a lower number of occurrences through grep/wc than Match.

Revision as of 05:48, 13 September 2013

Complementary Strand

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

6 Different Reading Frames

+1 Reading Frame

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

+2 Reading Frame

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

+3 Reading Frame

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

-1 Reading Frame

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

-2 Reading Frame

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

-3 Reading Frame

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

XMLPipeDB Match Practice

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

The command: java -jar xmlpipedb-match-1.1.1.jar "GO:000916." <493.P_falciparum.xml.

  • How many unique matches are there?

There are two unique matches.

  • How many times does each unique match appear?

go:0009165 appears twice and go:0009168 appears once.

  • What information do you think the pattern GO:000916. represents?

This pattern might represent the proteins in the organism Falciparum.

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

The command: java -jar xmlpipedb-match-1.1.1.jar "\"James.*\"" < 493.P_falciparum.xml.

  • How many unique matches are there?

There are two unique matches.

  • How many times does each unique match appear?

"james k.d." appears 8238 times and "james a.a." appears just once.

  • What information do you think the pattern \"James.*\" represents?

This pattern can represent the different labeled proteins.

  • 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. What answer does Match give you?

Match gives me 830101 for the occurrences of the pattern ATG in the file.

  • What answer does grep/wc give you?

Grep/wc gave me 502410 (lines), 502410 (words), and 35671048 (characters).

  • Do the answers make sense? Explain your response.

The answers for Match and grep/wc make sense because grep/wc gives us the number of occurrences in a line and counts them as one even if there's two combined, so it is expected to see a lower number of occurrences through grep/wc than Match.

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