Difference between revisions of "Laurmagee: Week 3"
From LMU BioDB 2013
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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
- First Reading Frame (+1)
- cat sequence_file | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed
- Second Reading Frame (+2)
- cat sequence_file | sed "s/^.//g" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed
- Third Reading Frame (+3)
- cat sequence_file | sed "s/^..//g" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed
- Fourth Reading Frame (-1)
- rev sequence_file | sed "y/atgc/tacg/" | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed
- 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
- 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
- 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.
-