Difference between revisions of "KSherbina Week 3"
From LMU BioDB 2013
(Added some notes about the command grep.) |
(Added some comments about using XMLPipeDB Match to find pattern within sequence.) |
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| Line 2: | Line 2: | ||
:<!-- . : means ''wildcard''; doesn't matter what nucleotides they are--> | :<!-- . : means ''wildcard''; doesn't matter what nucleotides they are--> | ||
:<!-- ^ : search for pattern at the beginning of a line--> | :<!-- ^ : search for pattern at the beginning of a line--> | ||
| + | |||
| + | <!--XMLPipeDB Match Practice Task 1--> | ||
| + | <!--java -jar xmlpipedb-match-1.1.1.jar "GO:000916." < 493.P_falciparum.xml--> | ||
| + | :<!-- : sending a file--> | ||
| + | <!--There are two unique matches. First one appears twice. Second one appears once.--> | ||
| + | |||
| + | <!--XMLPipeDB Match Practice Task 2--> | ||
| + | <!--java -jar xmlpipedb-match-1.1.1.jar \"James.*\" < 493.P_falciparum.xml--> | ||
| + | :<!--Double quotes are in the sequence to be searched so you need to precede the double quotes with \--> | ||
| + | :<!-- .* Match any number of characters after the symbol that came before | ||
| + | <!--There are two unique matches. First one appears 8238 times. Second one appears once.--> | ||
