BIO Assignment 1 2011

Note! This assignment is currently inactive. Major and minor unannounced changes may be made at any time.

 

 

   

Assignment 1 - Databases and Molecular Models

Introduction

In this assignment we will introduce some key databases for bioinformatics that we will refer to throughout the course. You will receive more information on these databases as the course progresses, but you should be familiar in principle with their contents and services from the outset. Also, to enhance your course experience, you should familiarize yourself with a molecular graphics viewer and practice viewing molecules in stereo.

Submission and due date

Prepare a Microsoft Word document with a title page that contains:

• your full name
• your Student ID
• your e-mail address

Copy the assessment part of the assignment into the document. save it with a filename of: A1_{lastname}.{firstname}.doc (for example my first assignment would be named: A1_steipe.boris.doc) and e-mail the document to boris.steipe@utoronto.ca before the due date. 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 Monday, October 1. at 11:00 in the morning.

Grading

Marks for this assignment are self assessed. We expect your honesty, but you can expect that the skills you obtain through this assignment will also be required for the final exam.

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 and an additional mark for every full twelve hour period past the due date. Assignments received more than 5 days past the due date will not be assessed. If you need an extension, you must arrange this beforehand.

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

   

NAR DB and Web Service issues (1 mark)

Familiarize yourself with the scope and breadth of the tools and resources that are available on the Web.

1. Access the 2007 NAR supplement issue on databases, browse the table of contents and read the abstract for at least one of the databases that you find particularly interesting. Follow the link to that database. Explore, and briefly note your experiences: was it clear what data is being maintained at the site? Was it clear how to use the database? Was it clear how this database could be useful for your research?
2. Access the 2007 NAR supplement issue on Web Services, browse the table of contents and read the abstract for at least one of the services that you find particularly interesting. Follow the link to that tool. Explore, and briefly note your experiences: was it clear what data the service uses, what it does and what its results mean? Was it clear how to use the service? Was it clear how this service could be useful for your research?

Entrez and the NCBI (2 marks)

The NCBI adminsters some of the world's most important databases, such as GenBank.

1. Access the NCBI website at http://www.ncbi.nlm.nih.gov/ Look for the site-map and browse the contents of this large site; find which databases and services are hosted here. Expect to spend at least half an hour to familiarize yourself with the site.
2. Access the Map viewer (under the Genomes section of the Databases division). Click on the link to Saccharomyces cerevisiae for a whole genome view, then click on the icon for chromosome IV for a more detailed view. Enter the region between 340,000 and 380,000 in the "Region shown" fields on the left. How many genes does this region contain? How many of these are protein genes?
   1. Click on MBP1 to follow the link to its Entrez Gene page. Study the contents of the page. If you are not clear what the sections show you, click on one of the question marks. If you are still not clear, ask on our mailing list.
      1. Follow the link to PubMed for this gene. You should find (at least) 25 publications. Click on the History tab to find the index of the query that got you here (eg. "#4"). Now search for those papers in your query that were published in 2007: enter #4 AND 2007[DP] into the search field and click "Go". Make yourself familiar with the Search field descriptions and tags (in particular [DP], [AU], [TI], and [TA]), how you use the History to combine searches, and the use of AND, OR, NOT and brackets.
   2. Back at the MapViewer pager, click on pr in the same row as the MBP1 gene to find a list of GenPept (protein) records for this gene. Follow the link to the RefSeq record for this protein: NP_010227. This is a flat-file record for the Mbp1 gene. Study the fields and the format. Then use the "Display" option in the header to show this protein sequence in a FASTA format, choose "send to ... Text" to get only the FASTA format. Make sure you understand the difference between GenBank/GenPept and RefSeq, between GI number, accession and locus (refer to the lecture slides as soon as they are posted).
3. In the header bar of the MapViewer, click on the link to Entrez. Enter mbp1 into the search field of the Entrez page and click "GO".
   1. Increase the relevance of returned items by restricting your search to a particular organism. Access and read the Help pages for Entrez and make sure you understand how to use limits and how to search in search field indexes. You will already have encountered similar concepts when you visited PubMed.
   2. Enter: mbp1 AND "saccharomyces cerevisiae"[organism] into the Entrez search field and click "GO". Click on the CoreNucleotide link of the results.
   3. The RefSeq sequence in these results is the entire yeast chromosome IV (1.5 Mbp) which you probably don't want to explore unless you actually want to. Check the list for a different record that contains only the gene's (full-length) nucleotide sequence. There are (as of this writing) two such records. Explore either one of the two, these are nucleotide sequences in the GenBank flat file format.

The EBI (1 mark)

In many ways the European EBI is complementary to the US NCBI. A data-sharing agreement for instance guarantees that the contents of the EMBL Nucleotide Sequence Database, GenBank and the Japanese DDBJ are synchronized on a daily basis. But there are of course also unique and uniquely valuable resources at the EBI.

1. Enter 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. Spend some time getting an idea of what is being offered here.
2. Visit the 2can education support portal at http://www.ebi.ac.uk/2can/home.html . Explore its offerings, in particular, follow the links Bioinformatics tutorials → Database browsing and read the section on the different interface systems. You have encountered Entrez previously, now find out more about SRS, BioMart and UniProt Search.
3. To learn more about the UniProt database: access the UniProt user manual at http://ca.expasy.org/sprot/userman.html and read through sections 1 and 2 of the manual.
   1. Contrast the contents of a Uniprot record with a GenPept record: for example MBP1_YEAST and NP_010227.
4. Follow the link to Ensembl, click on saccharomyces cerevisiae and then on chromosome IV. Access the regions from basepair 340000 to 380000; contrast the display with the NCBI MapViewer. Identify the Mbp1 gene and click on it to retrieve its Gene report (under the systematic name: YDL056W). Can you find your way from this Gene report to the expressed protein sequence?

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.

KEGG (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

Molecular graphics

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.

VMD (1 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

 

 

Copy and paste from the following for your submission. Copy the most appropriate phrase for each section, fill in the blanks and answer the questions truthfully.

 

1.1
NAR database issue:
I have explored the database TOC and explored the following database:
________________________. My comments on clarity of contents, usability
and utility are as follows:



(0.5 marks) / or: I did not find the time to explore one of the databases (0 marks).


NAR Web service issue:
I have explored the Web service TOC and explored the following tool:
________________________. My comments on clarity of contents, usability
and utility are as follows:



(0.5 mark) / or:  I did not find the time to explore one of the Web services (0 marks).

   

1.2
NCBI:
I have explored the NCBI Web site, familiarized myself with its
key databases and am confident that I will find information
that I am  looking for. I have also used the MapViewer, followed
a gene's annotations into PubMed and familiarized myself with 
PubMeds query syntax.
(1 mark) / or: I did not find the time to do this part of the assignment (0 marks).

Entrez:
I have explored the Entrez search page, and learned how to limit queries
and restrict searches. I am confident that I will find the information
that I am  looking for. The full-length yeast Mbp1 nucleotide sequence I found
has the accession number ____________ .
(1 mark) / or: I did not find the time to do this part of the assignment (0 marks).

   

1.3 EBI:
I have explored the EBI Web site, familiarized myself with its
contents and services and am confident that I will find information
that I am looking for. I have read the 2can tutorial on database browsing
and have read about the UniProt knowledgebase. Also, I have used the
Ensembl genome browser to access the Gene report for Mbp1. In order
to get from the Gene report to the protein sequence I have done the
following:


(1 mark) / or: I did not find the time to explore the EBI site and its offerings (0 marks).

   

1.4 the 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).

   

Copy and paste from the following statements the one that best characterizes your situation:

VMD:
I have successfully completed the first part of the VMD tutorial;
I understand the purpose and use of
all the forms used in the tutorial examples
and can confidently use the program for
my own visualization tasks (2 marks).

or

I have worked with the VMD tutorial. Nevertheless,
I am not confident with the forms and their use
and before I can use it for my own purposes
I will need additional training (1 mark).

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]