[[Image:ExPASy_Prokaryote.txt_Translation.png|ExPASy Translate Tool Results for prokaryote.txt DNA Sequence - Thank you, [[User:Bklein7|Brandon Klein]], for uploading the image.]]

[[Image:ExPASy_Prokaryote.txt_Translation.png|ExPASy Translate Tool Results for prokaryote.txt DNA Sequence - Thank you, [[User:Bklein7|Brandon Klein]], for uploading the image.]]

* '''Note:''' The amino acid sequences that I recovered from using text processing commands (and the Terminal app on my MacBook) are a match to the ExPASy Translate Tool results of the same DNA sequence from the ''prokaryote.txt'' file.

* '''Note:''' The amino acid sequences that I recovered from using text processing commands are a match to the ExPASy Translate Tool results of the same DNA sequence from the ''prokaryote.txt'' file.

=== XMLPipeDB Match Practice ===

=== XMLPipeDB Match Practice ===

For your convenience, the XMLPipeDB Match Utility (''xmlpipedb-match-1.1.1.jar'') has been installed in the ''~dondi/xmlpipedb/data'' directory alongside the other practice files. Use this utility to answer the following questions:

For your convenience, the XMLPipeDB Match Utility (''xmlpipedb-match-1.1.1.jar'') has been installed in the ''~dondi/xmlpipedb/data'' directory alongside the other practice files. Use this utility to answer the following questions:

# What Match command tallies the occurrences of the pattern <code>GO:000[567]</code> in the ''493.P_falciparum.xml'' file?

# What Match command tallies the occurrences of the pattern <code>GO:000[567]</code> in the ''493.P_falciparum.xml'' file? '''java -jar xmlpipedb-match-1.1.1.jar "GO:000[567]" < 493.P_falciparum.xml'''

#* How many unique matches are there?

#* How many unique matches are there?

#** There are '''3''' unique matches.

#** There are '''3''' unique matches.

#* How many times does each unique match appear?

#* How many times does each unique match appear?

#** "go:007" appears '''113''' times. "go:0006" appears '''1100''' times. "go:005" appears '''1371''' times.

#** "go:0007" appears '''113''' times. "go:0006" appears '''1100''' times. "go:0005" appears '''1371''' times.

# Try to find one such occurrence “in situ” within that file. Look at the neighboring content around that occurrence.

# Try to find one such occurrence “in situ” within that file. Look at the neighboring content around that occurrence.

#* Describe how you did this.

#* Describe how you did this.

#** First, I typed the command "grep "GO:005" 493.P_falciparum.xml" and it gave me a list that showed similar lines of code: <dbReference type="GO" id="GO:005....">. I typed the following command "cat 493.P_falciparum.xml" that allowed me to view the entire file, which is a very large file indeed. Then I manually scrolled through the file to find the pattern (lots of scrolling).

#** First, I typed the command "grep "GO:0005" 493.P_falciparum.xml" and it gave me a list that showed similar lines of code: <dbReference type="GO" id="GO:0005....">. I typed the following command "cat 493.P_falciparum.xml" that allowed me to view the entire file, which is a very large file indeed. Then I manually scrolled through the file to find the pattern (lots of scrolling).

#* Based on where you find this occurrence, what kind of information does this pattern represent?

#* Based on where you find this occurrence, what kind of information does this pattern represent?