Week 3
This journal entry is due on Friday, September 13, at midnight PDT. (Thursday night/Friday morning)
Contents |
- Store your journal entry in the shared Class Journal Week 3 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
- Link to your journal entry from your user page.
- Link back from the journal entry to your user page.
- NOTE: you can easily fulfill the links part of these instructions by adding them to your template and using the template on your user page.
- Sign your portion of the journal with the standard wiki signature shortcut (
~~~~). - Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).
Read (or Re-Read)
Reflect
After completing the readings above and activities below, answer the following questions:
- Did you complete the Where’s Your Stuff? exercise successfully (see below)? (by success, we mean that the computer behaved as described in that exercise) If things did not turn out as expected, what points do you think need further explaining or clarification?
- Did you succeed in connecting to the Keck lab?
- What do you think you need in order to grow more comfortable, confident, and effective with the command line and the practice tasks?
Individual Journal Assignment
- Store this journal entry as "username Week 3" (i.e., this is the text to place between the square brackets when you link to this page).
- Link from your user page to this Assignment page.
- Link to your journal entry from your user page.
- Link back from your journal entry to your user page.
- Don't forget to add the "Journal Entry" category to the end of your wiki page.
- Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.
Group Assignments, Individual Submissions
To help ease the learning curve, we have grouped the class into pairs and one trio. Please sit together in the lab this week, and work with each other as needed. However, continue to submit on an individual basis.
- Tauras—Dillon
- Kevin Meilak—Hilda
- Katrina—Stephen
- Kurt—Mitchell—Alina
- Lena—Lauren
- Viktoria—Miles
- Gabriel—Kevin McGee
Self-Correct Week 2
- Use the ExPASy Translate Tool to self-check your Week 2 work. As you’ll see below, this tool will also be useful for Week 3 so it will be good to get to know this site.
- Go back to your Week 2 assignment and make corrections to your work. Keep the incorrect sequence there and then place the correct sequence below it.
- Explain how/why you made the translation error.
- These corrections are due at midnight on Friday, September 20 (Thursday night/Friday morning).
Where’s Your Stuff?
- Open a text editor (Notepad or WordPad on Windows, TextEdit on Macs, gedit on Linux, to name a few; others are available for download, such as TextWrangler and Sublime Text) and create a file that contains the following text, verbatim (copy-paste suggested):
<!doctype html>
<html>
<head>
<meta charset="UTF-8" />
<title>Hello</title>
</head>
<body>
<h1>Hello File!</h1>
<p>This is a text file that contains HTML.</p>
</body>
</html>
- Save this file as a text file (.txt extension). If you see any options or controls pertaining to “rich text” or “HTML,” make sure to disable them. Double-click on your newly-saved file; the text editor should have opened it.
- Change this file’s extension to .html—remember that the computer may protest, since it is trying to protect novice users from making a mistake. Insist that you know what you’re doing. Take note of the icon after renaming the file—did it change?
- Double-click on the renamed file; a web browser should open it now, and instead of code, you should see a very simple web page.
- Answer the “after” reflection questions above.
The Genetic Code, by Computer
Connect to the Keck lab as described in the Keck Lab Workstation Guidelines page of this wiki, and do the following exercises from there.
For these exercises, two files are available in the Keck lab system for practice; of course, you can always make your own sequences up. The practice files are ~dondi/xmlpipedb/data/prokaryote.txt and ~dondi/xmlpipedb/data/infA-E.coli-K12.txt.
Complement of a Strand
Write a sequence of piped text processing commands that, when given a nucleotide sequence, returns its complementary strand. In other words, fill in the question marks:
cat sequence_file | ?????
For example, if sequence_file contains:
agcggtatac
Then your text processing commands should display:
tcgccatatg
Reading Frames
Write 6 sets of text processing commands that, when given a nucleotide sequence, returns the resulting amino acid sequence, one for each possible reading frame for the nucleotide sequence. In other words, fill in the question marks:
cat sequence_file | ?????
You should have 6 different sets of commands, one for each possible reading frame. For example, if sequence_file contains:
agcggtatac
Then your text processing commands for 5’-3’ frame 1 should display:
SGI
Your text processing commands for 5’-3’ frame 3 should display:
RY
...and so on.
- Hint 1: The 6 sets of commands are very similar to each other.
- Hint 2: Under the ~dondi/xmlpipedb/data directory in the Keck lab, you will find a file called genetic-code.sed. To save you some typing, this file has already been prepared with the correct sequence of sed commands for converting any base triplets into the corresponding amino acid. For example, this line in that file:
s/ugc/C/g
...corresponds to a uracil-guanine-cytosine sequence transcribing to the cysteine amino acid (C). The trick is to figure out how to use this file to your advantage, in the commands that you'll be forming.
Check Your Work
Fortunately, online tools are available for checking your work; we recommend the ExPASy Translate Tool, sponsored by the same people who run SwissProt. You're free to use this tool to see if your text processing commands produce the same results.
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:
- What Match command tallies the occurrences of the pattern GO:000916. in the 493.P_falciparum.xml file?
- How many unique matches are there?
- How many times does each unique match appear?
- 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?
- How many unique matches are there?
- How many times does each unique match appear?
- What information do you think the pattern \"James.*\" represents?
- 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?
- What answer does grep/wc give you?
- Do the answers make sense? Explain your response.
