BIO Assignment Week 3

Assignment for Week 3
Sequence Analysis

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

 
 

Concepts and activities (and reading, if applicable) for this assignment will be topics on next week's quiz.

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.

VMD

Task:

• Access the VMD page.
• Install the program as per the instructions in the section: "Installing VMD".
• In the tutorial section work through
  • Part 1 (Introduction), and
  • Part 2 (Working with a single molecule).

Stereo vision (1 mark):=

Task:

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

Practice at least ...

• two times daily,
• for 3-5 minutes each session,

Keep up your practice throughout the course. Stereo viewing will be required in the final exam, but more importantly, it is a wonderful skill that will greatly support any activity of yours related to structural molecular biology. Practice with different molecules and try out different colours and renderings.

Note: do not go through your practice sessions mechanically. If you are not making any progress with stereo vision, contact me so we can help you on the right track.

R

The R statistics environment and programming language is an exceptionally well engineered, free (as in free speech) and free (as in free beer) platform for data manipulation and analysis. The number of functions that are included by default is large, there is a very large number of additional, community-generated analysis modules that can be simply imported from dedicated sites (e.g. the Bioconductor project for molecular biology data), or via the CRAN network, and whatever function is not available can be easily programmed. The ability to filter and manipulate data to prepare it for analysis is an absolute requirement in research-centric fields such as ours, where the strategies for analysis are constantly shifting and prepackaged solutions become obsolete almost faster than they can be developed. Besides numerical analysis, R has very powerful and flexible functions for plotting graphical output.

R is not a main focus of the course, but an important tool I would like you to pick up "on the side".

Task:

• Access the R tutorial on this site.
• Work through the sections Installation, User interface, and Packages.