BIO Assignment 2 2011
Contents
Assignment 2 - Search, retrieve and annnotate
Note: This assignment is currently inactive. Unannounced changes may be made at any time.
Introduction
Baker's yeast, Saccharomyces cerevisiae, is perhaps the most important model organism since it is a eukaryote that has been studied genetically and biochemically in great detail for many decades and it is easily manipulated with high-throughput experimental methods. We will use information from this model organism to study the conservation of function and sequence in other fungi whose genomes have been completely sequenced. This and the following assignments will revolve around a transcription factor that plays an important role in the regulation of the cell cycle: Mbp1, a key component of the MBF complex (Mbp1/Swi6) that regulates gene expression at the crucial G1/S-phase transition of the mitotic cell cycle and has been shown to bind to the regulatory regions of more than a hundred target genes.
One would assume that such control machinery would be conserved in other fungi and it will be your task in these assignments to collect evidence whether related molecular machinery is present in some of the newly sequenced fungal genomes.
(If you need to brush up on the concepts mentioned above, you could study the corresponding chapter in Lodish's Molecular Cell Biology. It is not strictly necessary to understand the details of the yeast cell-cycle to complete the assignments, but highly recommended, if this all is to make some sense.)
In this particular assignment you will go on a search and retrieve mission for information and annotation of Mbp1 homologues in a fungal genome, using common public databases and Web resources.
Preparation, submission and due date
Read carefully. Be sure you have understood all parts of the assignment and cover all questions in your answers! Sadly, we always get assignments back in which important aspects have simply been overlooked and marks are unnecessarily lost. Sadly, we always get assignments back in which important aspects have simply been overlooked and marks are unnecessarily lost. If you did not notice that the above sentence was repeated, you are not reading carefully enough.
Prepare a Microsoft Word document with a title page that contains:
- your full name
- your Student ID
- your e-mail address
- the organism name you have been assigned (see below)
Follow the steps outlined below. You are encouraged to write your answers in short answer form or point form, like you would document an analysis in a laboratory notebook. However, you must
- document what you have done,
- note what Web sites and tools you have used,
- paste important data sequences, alignments, information etc.
If you do not document the process of your work, we will deduct marks. Try to be concise, not wordy! Use your judgement: are you giving us enough information so we could exectly reproduce what you have done?
Write your answers into separate paragraphs and give each its title. Save your document with a filename of:
A2_{lastname}.{firstname}.doc
(for example my first assignment would be named: A2_steipe.boris.doc - and don't include the brackets this time, please!)
Finally e-mail the document to [boris.steipe@utoronto.ca] before the due date.
Your document must not contain macros. Please turn off and/or remove all macros from your Word document; we will disable macros, since they pose a security risk.
With the number of students in the course, we have to economize on processing the assignments. Thus we will not accept assignments that are not prepared as described above. If you have technical difficulties, contact me.
The due date for the assignment is Thursday, October 19. at 10:00 in the morning.
Grading
Don't wait until the last day to find out there are problems! Assignments that are received past the due date will have one mark deducted at the first minute of every twelve hour period past the due date. Assignments received more than 5 days past the due date will not be assessed.
Marks are noted below in the section headings for of the tasks. A total of 10 marks will be awarded, if your assignment answers all of the questions. A total of 2 bonus marks (up to a maximum of 10 overall) can be awarded for particularily interesting findings, or insightful comments. A total of 2 marks can be subtracted for lack of form or for glaring errors. The marks you receive will
- count directly towards your final marks at the end of term, for BCH441 (undergraduates), or
- be divided by two for BCH1441 (graduates).
Key databases
The NCBI (1 mark)
Visit the NCBI website at http://www.ncbi.nlm.nih.gov/
Look for the site-map and explore the contents of this site, the databases, the services and its other offerings. Browse across the different sections and set yourself a specific objective so you are confident you know what this part is and does. Expect to spend more than two hours on this task.
For example, you might have:
- looked at least at two Coffee Break tutorials and know what the others contain
- familiarized yourself with the search field tags in PubMed to the degree that you know how to formulate a specific search, for example to retrieve review articles that mention the cell cycle in their title, which are about saccharomyces cerevisiae , that are not more than two years old
- tried searching for crossreferences to the YER111C gene using the Entrez system
- used the map viewer to explore the region between 370 and 400 KB on yeast chromosome V
- etc.
The EBI (1 mark)
Visit the EBI website at http://www.ebi.ac.uk/
Look for the site-map and explore the contents of this site, the databases, the services and its other offerings. Browse across the different sections and set yourself specific objectives so you are confident you know what each section is and does. Expect to spend more than two hours on this task.
For example, you might have:
- browsed through the tutorials (e.g. the lectin tutorial) in the education section of the Macromolecular Structure Database (MSD)group
- used the e! Ensembl browser to compare your experience in exploring yeast chromosomeV:370000-400000
- explored crossreferences to the yeast Swi4 protein using the SRS system
- browsed through the Interpro Molecule of the Month articles and read the article on TATA-box binding protein
- looked at the 2can tutorial pages and explored the tutorial on database browsing
- etc.
The PDB (1 mark)
Visit the PDB website at http://www.pdb.org/
Browse across the different sections and set yourself a specific objective so you are confident you know what this part is and does. Look for the "About PDB" page and explore the page. Explore the links on the "Education" page to see where you might fill in gaps in your knowledege of structural molecular biology. From the homepage, find a protein of your choice (eg. the yeast Swi6 or Mbp1 protein) and explore the information that is available for it. Expect to spend more than an hour on this task.
For example, you might have:
- worked through the PDB query tutorial
- browsed through the Molecule of the Month articles and studied the entry on TATA-box binding proteins
- and explored structures entries for 1SW6, 1E0B and 1BM8
- etc.
BioMart (1 mark)
Data integration across a variety of databases is a major challenge for the data-management side of bioinformatics. You have come across two solutions above: the NCBI Entrez system and the EBI SRS system. Here is another solution to this problem: the EBI BioMart system.
- Access the BioMart server at http://www.biomart.org
- Follow at least two links into BioMart databases (e.g. ensembl and HapMap)
- Explore
Rasmol (3 marks)
Access the Rasmol tutorial at http://biochemistry.utoronto.ca/steipe/bioinformatics/tutorials/rasmol_tutorial.html Install Rasmol(Linux), RasMac (Macintosh), or RasTop(Windows) on your computer.
Work through the tutorial.
Stereo vision (3 marks):
Use the hints given in the stereo vision section of the Rasmol tutorial and practice viewing molecules in stereo. Make sure that you use the Rasmol command
set stereo -5
to display molecules for divergent ("wall-eyed", not "cross-eyed") stereo view. Practice at least ...
- two times daily,
- for 3-5 minutes each session,
- for at least twelve days (twentyfour sessions) between now and the due date of the assignment.
Keep up your practice after the assignment. Stereo viewing will be required in the final exam.
You will receive 1 mark for every 8 sessions (4 days) of practice you have completed (max. 3 marks). Use different molecules and try them with different colouring and renderings. You will find a list suggesting interesting molecules on the tutorial page.
Record your progress on a sheet of paper. Make sure you also record the information for the supplementary questions you need to turn in (see below).
Note: do not go through this assignment mechanically. If you are not making any progress, contact me so we can help you on the right track.
Assessment
NCBI: I have explored the NCBI Web site in detail, familiarized myself with its contents and am confident that I will find information that I am looking for. A part of the site that I found particularily interesting or useful is ________________________ (1 mark).
or
I did not find the time to explore the NCBI site in detail (0 marks).
EBI: I have explored the EBI Web site in detail, familiarized myself with its contents and am confident that I will find information that I am looking for. A part of the site that I found particularily interesting or useful is ________________________ (1 mark).
or
I did not find the time to explore the EBI site in detail (0 marks).
PDB: I have explored the PDB Web site in detail, familiarized myself with its contents and am confident that I will find information that I am looking for. A part of the site that I found particularily interesting or useful is ________________________ (1 mark).
or
I did not find the time to explore the PDB site in detail (0 marks).
BioMart: I have accessed the BioMart Web site and familiarized myself with the functionality of at least two BioMart databases. I understand some of the issues of data integration and how they are addressed through BioMart. (1 mark).
or
I did not find the time to explore the seqhound site (0 marks).
Copy and paste from the following statements the one that best characterizes your situation:
Rasmol: I have successfully completed the Rasmol tutorial; I understand the purpose and command syntax of all the commands used in the scripted tutorial examples and can confidently use all of these for my own visualization tasks (3 marks).
or
I have worked with the Rasmol tutorial. Nevertheless, I am not confident with the purpose and command syntax of some of the commands used in the scripted tutorial examples. I have changed some parameters and achieved predictable results (2 marks).
or
The command syntax of some of the commands used in the scripted tutorial examples is challenging; I have worked with the program, but before I can use it for my own purposes I will need additional training (1 marks).
or
I have not done this part of the assignment (0 marks).
Copy the following statement into your assignment and fill in the blanks truthfully.
Stereo Vision: I have practiced stereo viewing twice daily on _____ days for a total of _____ practice sessions (maximum 3 marks for 24 sessions).
Supplementary questions (these will not be marked):
I have been able to visualize a 3D image in focus for the first time on day ___. I have been able to view molecules in stereo comfortably since day ___. Currently I am able to view molecules in stereo on screen and on paper with ease / with some effort / with difficulty / rarely / not at all.
[End of assignment]
