Jwoodlee Week 3

Electronic Lab Notebook

ssh into my.cs.lmu.edu using your username, and enter your password.

Complement of a Strand

locate the file in ~dondi/xmlpipedb/data, and enter the following command:

cat prokaryote.txt | sed “y/actg/tgac”

This will yield prokaryote.txt’s complementary DNA strand.

Reading Frames

These sets of commands are more complicated than Complement of a Strand. This is essentially what I had to accomplish:

take sequence file, replace the t’s with u’s, break up the sequence into groups of 3, use genetic-code.sed as the translation “chart”, and then eliminate extra nucleotides if there are any. For the different reading frames I will just delete the first one or two nucleotides

After lots of googling I came up with this basic outline in terminal:

cat prokaryote.txt | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed

For different reading frames, insert sed “s/^.//g” or "s/^..//g" after prokaryote.txt, and of course in order to use a different DNA sequence prokaryote.txt would be different. The following commands will be written exactly and should return the correct output. Enter these commands into terminal after navigating to nfs/home/dondi/xmlpipedb/data/.

+1
cat prokaryote.txt | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[acug]//g"

+2
cat prokaryote.txt | sed "s/^.//g" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[acug]//g"

+3 
cat prokaryote.txt | sed "s/^..//g" | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[acug]//g"

In order to do these frames, I transcribed the DNA using sed "y///" and then reversed them in order to translate them from the proper side. (5' --> 3')

-1
cat prokaryote.txt | sed "y/actg/tgac/" | rev | sed "s/t/u/g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[acug]//g"

-2
cat prokaryote.txt | sed "y/actg/tgac/" | rev | sed "s/t/u/g" | sed "s/^.//g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[acug]//g" 

-3
cat prokaryote.txt | sed "y/actg/tgac/" | rev | sed "s/t/u/g" | sed "s/^..//g" | sed "s/.../& /g" | sed -f genetic-code.sed | sed "s/[acug]//g" 

Checked with Expasy translation tool.

For the XMLPipeDB utility I used the wiki provided on the course website. The first command I found on the wiki after scrolling down to the "Running Command-Line Java Programs" section. I entered the commands into the command prompt window under the directory, ~dondi/xmlpipedb/data, this allowed me to use the XMLPipeDB utility.

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:

1. What Match command tallies the occurrences of the pattern GO:000[567] in the 493.P_falciparum.xml file?
   • Using the wiki page I found this command and ran it in ~dondi/xmlpipedb/data
   • java -jar xmlpipedb-match-1.1.1.jar GO:000[567] < 493.P_falciparum.xml
   • How many unique matches are there?
   • I read the output of the function, and wrote it here.
     • Total Unique Matches: 3
   • How many times does each unique match appear?
     • More reading of output brought me to this spot, and I wrote it down after clicking on "edit" on this wiki page.
     • go:0007: 113
     • go:0006: 1100
     • go:0005: 1371
2. Try to find one such occurrence “in situ” within that file. Look at the neighboring content around that occurrence.
   • One such occurrence: <dbReference type="GO" id="GO:0005777">
   • Describe how you did this.
     • I entered grep "GO:000[567]" 493.P_falciparum.xml | more, as a command and then picked out a random occurrence. I then edited the wiki page and wrote it down.
   • Based on where you find this occurrence, what kind of information does this pattern represent?
     • The ID of the gene ontology within a database, or an identifier of a gene ontology term. I found this out on the match utility wiki page.
3. What Match command tallies the occurrences of the pattern \"Yu.*\" in the 493.P_falciparum.xml file?
   • Entered this command into terminal, have not changed directories.
   • java -jar xmlpipedb-match-1.1.1.jar \"Yu.*\" < 493.P_falciparum.xml
   • How many unique matches are there?
     • Read output and jotted it down here.
     • 3
   • How many times does each unique match appear?
     • "yu b.": 1
     • "yu k.": 228
     • "yu m.": 1
   • What information do you think this pattern represents?
     • I used grep on the same pattern to try to figure this out and based on what I found, I would say it is somebody's name.
4. Use Match to count the occurrences of the pattern ATG 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?
     • atg: 830101
     • Total unique matches: 1
   • What answer does grep + wc give you?
     • 502410 502410 35671048 from left to right: lines, words, bytes
   • Explain why the counts are different. (Hint: Make sure you understand what exactly is being counted by each approach.)
     • grep + wc counts the lines with at least one occurrence of "ATG" while the Match utility counts each individual instance of "ATG". Therefore grep+wc gets a lower number for word count.

BIOL 367, Fall 2015, User Page, Team Page

Weekly Assignments	Individual Journal Pages	Shared Journal Pages
Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 Week 14 Week 15	Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 Week 14 Week 15	Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9