Difference between revisions of "HDelgadi Week 3"
From LMU BioDB 2013
(complementary strand update) |
(Adding the amino acids for the six reading frames) |
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| − | *Complementary Strand | + | * Complementary Strand |
cat seq_file | sed "y/tagc/atcg/" | cat seq_file | sed "y/tagc/atcg/" | ||
| + | |||
| + | * 6 Different Reading Frames | ||
| + | |||
| + | *# cat sequence_file | sed "s/.../&/g" | sed "s/t/u/g" | sed genetic-code.sed | ||
''' XMLPipeDB Match Practice ''' | ''' XMLPipeDB Match Practice ''' | ||
Revision as of 23:58, 12 September 2013
- Complementary Strand
cat seq_file | sed "y/tagc/atcg/"
- 6 Different Reading Frames
- cat sequence_file | sed "s/.../&/g" | sed "s/t/u/g" | sed 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?
- 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?
