Difference between revisions of "Laurmagee: Week 3"

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(Finished Reading Frames)
(Added XMLPipeDB Information)
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==XMLPipeDB Match Practice==
 
==XMLPipeDB Match Practice==
#
+
#You must use the MATCH command java -jar xmlpipedb-match-1.1.1.jar "GO:000916." <493.P_falciparum.xml. to find the occurrences of the pattern in the file.
#*
+
#*The MATCH command finds two unique solutions.
#*
+
#*The pattern "go:0009165" appears twice and "go:0009168" appears once.
#*
+
#
+
#*
+
 
#*
 
#*
 +
#You must use the MATCH command java -jar xmlpipedb-match-1.1.1.jar "\"James.*\"" < 493.P_falciparum.xml to find the occurrences of the pattern in the file.
 +
#*The MATCH command finds two unique solutions.
 +
#*The pattern "james k.d." appears 8238 times and "james a.a." appears once.
 
#*
 
#*
 
#
 
#

Revision as of 22:29, 12 September 2013

Complement of a Strand

  • The appropriate processing commands are the following: cat sequence_file | sed "y/atgc/tacg/"
  • This will turn a nucleotide sequence, "agcggtatac", into "tcgccatatg", it's compliment.

Reading Frames

  1. First Reading Frame (+1)
    • cat sequence_file | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed
  2. Second Reading Frame (+2)
    • cat sequence_file | sed "s/^.//g" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed
  3. Third Reading Frame (+3)
    • cat sequence_file | sed "s/^..//g" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed
  4. Fourth Reading Frame (-1)
    • rev sequence_file | sed "y/atgc/tacg/" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed
  5. Fifth Reading Frame (-2)
    • rev sequence_file | sed "y/atgc/tacg/" | sed "s/^.//g" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed
  6. Sixth Reading Frame (-3)
    • rev sequence_file | sed "y/atgc/tacg/" | sed "s/^..//g" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed

XMLPipeDB Match Practice

  1. You must use the MATCH command java -jar xmlpipedb-match-1.1.1.jar "GO:000916." <493.P_falciparum.xml. to find the occurrences of the pattern in the file.
    • The MATCH command finds two unique solutions.
    • The pattern "go:0009165" appears twice and "go:0009168" appears once.
  2. You must use the MATCH command java -jar xmlpipedb-match-1.1.1.jar "\"James.*\"" < 493.P_falciparum.xml to find the occurrences of the pattern in the file.
    • The MATCH command finds two unique solutions.
    • The pattern "james k.d." appears 8238 times and "james a.a." appears once.
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