BIO Assignment 1 2011

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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.

Preparation, submission and due date

Read carefully.

Be sure you have understood all parts of the assignment and cover all questions in your answers!

Review the guidelines for preparation and submission of BCH441 assignments.

The due date for the assignment is Thursday, September 25 at 10:00 in the morning.

   

   

Key databases

   

Entrez and the NCBI (1 mark)

The NCBI administers some of the world's most important databases, such as GenBank. In this section you should

• Explore the NCBI Web site, familiarize yourself with its key databases and explore the resources to become confident that you will find information that you are looking for.
• Follow a protein's annotations into PubMed and familiarize yourself with PubMed's query syntax.
• Explore the Entrez search page, and learn how to limit queries and restrict searches

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 under Saccharomyces cerevisiae (Build 2.1) 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) 27 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 2008: enter #4 AND 2008[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 record listed in the results contains the entire yeast chromosome IV (1.5 Mbp) which you probably don't want to explore unless you actually want to. The result is correct, since mbp1 is one of the 787 genes annotated on that chromosome, but perhaps not what we had in mind when we queried for a nucleotide sequence of the mbp1 gene. Check the results for a different record that contains only the mbp1 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.

Document your activities in point form.

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. In this part of the assignment

• you should explore the EBI Web site, familiarize yourself with its contents and services and explore the resources to become confident you will find information that you are looking for.
• You should read the 2can tutorial on database browsing and the UniProt knowledgebase.
• You should compared a UniProt record with the corresponding GenPept record and use the ensembl browser to access a gene report.

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). Find your way from this Gene report to the expressed protein sequence and list the steps you have gone through.

Document your activities in point form.

The PDB (1 mark)

Visit the RCSB PDB website at http://www.pdb.org/ , explore the database and familiarize yourself with its contents.

1. Look for the "Getting started" page and explore the page.
2. Explore the links on the "Education" page to see where you might fill in gaps in your knowledege of structural molecular biology, such as the Biological Units tutorial; read up on one or two the excellent molecule of the month articles, such as the TATA binding protein (July 2005).
3. From the homepage, search for the yeast Mbp1 protein (by keyword) and explore the information that is available in one of the entries that was retrieved.

Document your activities in point form.

     

Molecular graphics

VMD

Access the VMD tutorial. Work through parts 1 (installation) and 2 (basic visualization).

Stereo vision (1 mark):

Access the Stereo Vision tutorial and practice viewing molecular structures in stereo.

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. Practice with different molecules and try out different colours and renderings.

You will receive 1 mark if you have completed at least 2 practice sessions per day of at least 5 minutes per session, twice daily.

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 with stereo vision, contact me so we can help you on the right track.

Supplementary questions (these will not be marked):

• In which session have you been able to visualize a 3D image in focus for the first time?
• From which session on have you been able to view molecules in stereo comfortably?
• How are you currently doing - can you view molecules in stereo on screen and on paper with ease / with some effort / with difficulty / rarely / not at all?

 

 

[End of assignment]