Week 4

This journal entry is due on Tuesday, September 29, at midnight PDT. (Monday night/Tuesday morning)

Overview

The purpose of this assignment is:

• To advance your text matching and manipulation skills at the command line.
• To reinforce what you have learned so far about transcription and translation.

Individual Journal Assignment

• Store this journal entry as "username Week 4" (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.
• For your assignment this week, you will keep an electronic laboratory notebook on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

Homework Partners

For most weeks in the semester, you will be assigned a "homework partner" from the complementary biology or computer science discipline. You will be expected to consult with your partner, sharing your domain expertise, in order to complete the assignment. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed). Homework partners for this week are:

• Mary Alverson, Mahrad Saeedi
• Nicole Anguiano, Veronica Pacheco
• Brandon Klein, Kristen Zebrowski
• Josh Kuroda, Emily Simso
• Ron Legaspi, Anindita Varshneya
• Trixie Roque, Elena Olufson
• Jake Woodlee, Brandon Litvak
• Kevin Wyllie, Erich Yanoschik

Transcription and Translation “Taken to the Next Level”

This computer exercise examines gene expression at a much more detailed level than before, requiring knowledge in both the biological aspects of the process and the translation of these steps into computer text-processing equivalents.

The following sequence represents a real gene, called infA and found in E. coli K12. As you might have guessed, it’s stored as infA-E.coli-K12.txt in ~dondi/xmlpipedb/data.

ttttcaccacaagaatgaatgttttcggcacatttctccccagagtgttataattgcggtcgcagagttggttacgc
tcattaccccgctgccgataaggaatttttcgcgtcaggtaacgcccatcgtttatctcaccgctcccttatacgtt
gcgcttttggtgcggcttagccgtgtgttttcggagtaatgtgccgaacctgtttgttgcgatttagcgcgcaaatc
tttacttatttacagaacttcggcattatcttgccggttcaaattacggtagtgataccccagaggattagatggcc
aaagaagacaatattgaaatgcaaggtaccgttcttgaaacgttgcctaataccatgttccgcgtagagttagaaaa
cggtcacgtggttactgcacacatctccggtaaaatgcgcaaaaactacatccgcatcctgacgggcgacaaagtga
ctgttgaactgaccccgtacgacctgagcaaaggccgcattgtcttccgtagtcgctgattgttttaccgcctgatg
ggcgaagagaaagaacgagtaaaaggtcggtttaaccggcctttttattttat

For each of the following questions pertaining to this gene, provide (a) the actual answer, and (b) the sequence of text-processing commands that calculates this answer. Specific information about how these sequences can be identified is included after the list of questions.

1. Modify the gene sequence string so that it highlights or “tags” the special sequences within this gene, as follows (ellipses indicate bases in the sequence; note the spaces before the start tag and after the end tag):
   • -35 box of the promoter

     ... <minus35box>...</minus35box> ...

   • -10 box of the promoter

     ... <minus10box>...</minus10box> ...

   • transcription start site

     ... <tss>...</tss> ...

   • ribosome binding site

     ... <rbs>...</rbs> ...

   • start codon

     ... <start_codon>...</start_codon> ...

   • stop codon

     ... <stop_codon>...</stop_codon> ...

   • terminator

     ... <terminator>...</terminator> ...

2. What is the exact mRNA sequence that is transcribed from this gene?
3. What is the amino acid sequence that is translated from this mRNA?

Supplementary Information

As a sample answer for the first question, Week 2’s paper handout sequence would have been marked as follows (line breaks are included only for clarity):

agtgta <minus35box>ttgaca</minus35box> tgatagaagcactctac <minus10box>tatatt</minus10box> tcaat
<tss>a</tss> ttcctag <rbs>gagg</rbs> tttgacct <start_codon>atg</start_codon> attgaacttgaa...aataccatggta
<stop_codon>taa</stop_codon> ccca <terminator>gccgccagttccgctggcggcatttt</terminator> aac

Note: The commands needed to generate the output above will be similar, but not exactly the same as the ones needed for infA.

Base your commands on the following hints/guidelines about the gene, plus your own knowledge learned from the past few weeks:

• The consensus sequence for the -10 site is [ct]at[at]at.
• The consensus sequence for the -35 site is tt[gt]ac[at].
• The ideal number of base pairs between the -35 and -10 box is 17, counting from the first nucleotide after the end of the -35 sequence up to the last nucleotide before the -10 sequence.
• The transcription start site is located at the 12th nucleotide after the first nucleotide of the -10 box.
• A consensus sequence for the ribosome binding site is gagg.
• The first half of the terminator “hairpin” is aaaaggt, where the u in the mRNA binds with a g instead of the usual a.
• The terminator includes 4 more nucleotides after the hairpin completes.

Computer Tips

• Remember that sed is line-based, and that you can add and count lines to get certain things done, say strictly before or after a certain point.
• Don’t forget how you enforced reading frames in Week 3.
• If you do add lines or spaces to get the job done, make sure to clean up after yourself by removing them from the final answer.
• This exercise is difficult enough that you might be thinking to yourself, “I’d rather do this by hand!” This sentiment is understandable, but when you find yourself feeling this way, consider the following:
  • Part of the difficulty is learning these things for the first time. Once you’ve gotten the hang of it, there’s no way that doing things by hand will be faster.
  • Consider trying to do this over and over, for multiple genes, with lots of potential variations. Doing this by hand not only takes longer at this point, but risks errors that a computer won’t make (once the correct commands have been determined).
• Form your commands so that they can be strung together into a single pipeline of processing directives in the end. In other words, once you’ve figured out how to do each step, no human intervention should be needed to perform everything from beginning to end.
• You will need the More Text Processing Features wiki page to complete this assignment. The How to Read XML Files wiki page gives you an idea for why the requested output was formatted the way it was.

Shared Journal Assignment

• Store your journal entry in the shared Class Journal Week 4 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

• This week we focus on additional sections from “What is Code?”: “Why are Programmers So Intense About Languages?” and “Why are Coders Angry?” (uh, are you?)

Reflect

1. Based on what you read here, would you consider sed to be a language? Why or why not?
2. Of the languages that are skimmed in these sections, which one (in the brief exposure this article gives) appeals to you the most, and why? (yes, we are also expecting the biology majors to answer this—no obligation to fully understand the languages nor examples; just share what you like about what you see)
3. Would you agree that coders are “angry?” Are biologists “angry” too? Why do you think so? (quid pro quo—computer scientists should answer this also, to the degree that you know biology and biologists)