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'''

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.

#* 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?

#** Firstly, the file appears to contain a database of genome sequences of the Parasite Plasmodium falciparum in which many people contributed to the study of this particular species of parasite. Looking at the pattern closely and in its place within the information presented in the file there are many "<dbReference type=..."> that leads me to believe that the pattern is a way to show relationships between the many different genome sequences. <dbReference type="GO" id="GO:0005..."> is just one of the many ways to relate genome sequences to one another.

#** Firstly, the file appears to contain a database of genome sequences of the Parasite Plasmodium falciparum in which many people contributed to the study of this particular species of parasite. Looking at the pattern closely and in its place within the information presented in the file there are many "<dbReference type=..."> that leads me to believe that the pattern is a way to show relationships between the many different genome sequences. <dbReference type="GO" id="GO:0005..."> is just one of the many ways to relate genome sequences to one another.

# What Match command tallies the occurrences of the pattern <code>\"Yu.*\"</code> in the ''493.P_falciparum.xml'' file?

# What Match command tallies the occurrences of the pattern <code>\"Yu.*\"</code> in the ''493.P_falciparum.xml'' file? '''java -jar xmlpipedb-match-1.1.1.jar "\"Yu.*\"" < 493.P_falciparum.xml'''

java -jar xmlpipedb-match-1.1.1.jar "\"Yu.*\"" < 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.

#** The information offers the last name and the first initial of a person who contributed to the sequencing of a human malaria parasite plasmodium falciparum.

#** The information offers the last name and the first initial of a person who contributed to the sequencing of a human malaria parasite plasmodium falciparum.

# Use Match to count the occurrences of the pattern <code>ATG</code> in the ''hs_ref_GRCh37_chr19.fa'' file (this may take a while).  Then, use '''grep''' and '''wc''' to do the same thing.

# Use Match to count the occurrences of the pattern <code>ATG</code> in the ''hs_ref_GRCh37_chr19.fa'' file (this may take a while).  Then, use '''grep''' and '''wc''' to do the same thing.

#* What answer does Match give you?

#* What answer does Match give you?