COSC 348: Lab02

Overview: Finding Data

An important part of bioinformatics is processing data, so the first thing we need to find out is "where is the data".

The purpose of this lab is to find information about the single protein called GABRA1, and the DNA sequence that is responsible for GABRA1 generation. In the second part, we'll look into how to find information about the whole genome.

IMPORTANT: Save the last 30 min or so for writing a 1 page report reflecting on your today's investion and submit it. Answering the questions provided along this document will help you to write it, do not hesitate about speculating, it is not an exam. Any feedback you provide regarding the lab session will be very valuable as well.
Remember, your today's lab work and this reflection are worth 1% of your final mark.

Part 1: Protein and DNA sequence retrieval

We will retrieve various information about the protein denoted by GABRA1.
First let us find out what the GABRA1 protein is: have a read of this.

Make sure you understand what GABRA1 is -- talk to someone near you, and see if you have the same idea.

ExPASy (SwissProt database) – retrieving the AA sequence of proteins

Now that we know what GABRA1 is, we want to find out, and store, the sequence of Amino Acids (AA) that makes the protein.

• Visit the ExPASy site at:   www.expasy.org/sprot
• Search List of UniProtKB/Swiss-Prot entries for "GABRA1" in the search text box.
• Click on the search result GBRA1_HUMAN, accession number P14867, and explore what kind of information is available about this protein.
  • Find out how many AA are in sequence of this protein?
  • Where in the cell would you expect to find this protein?
  • Based on publications titles can you name 3-5 disorders in which mutations of GABRA1 gene are involved?
  Make sure you are back on the GBRA1_HUMAN page.
• Find the section called Sequence and select "FASTA"
  This opens a page with the AA sequence presented in FASTA format.
  Save this to a text file.
  When reading the file -- use a fixed width font, such as Courier or Courier New Font

GenBank – Retrieving the coding DNA sequence for a protein

• Return to the GBRA1_HUMAN page
• On the left, click the 'cross-references' link, to take you halfway down the page.
• For the retrieval of the DNA coding sequence for our protein GABRA1, first choose GenBank from the dropdown menu on the left and then click the link X14766 mRNA, which will bring the GenBank entry for the human mRNA/gene encoding the GABRA1.
• Scroll down to the entry entitled ORIGIN, and notice that the DNA/mRNA sequence has 1742 bases whereas the protein GABRA1 has only 456 AA.
  
  • How many AA would you expect to find in a protein sequence from a 1742 nucleotides long mRNA?
  • Can you explain why? What is going on?
  • Can you figure out what the 'CDS' entry means?

This format of sequence is called the GenBank format.

By now, you should be ready to retrieve the same information for any gene/protein. Try with the Human Haemoglobin subunit alpha, and see if you can answer some of the following questions.

• How long is the subunit?
• What is its main function?
• Is its malfunction associated with any known disease?
• Can you retrieve a high-resolution X-ray structure? (Shortcut)

Part 2: Genome retrieval

Let us first see the genome in action. How viruses inject their RNA or DNA into our cells and thus force them to make more viruses. Life cycle of viruses in video.

GenBank – finding and retrieving genomes of viruses

GenBank – the leading nucleotide sequence repository/database maintained jointly by the NCBI (U.S. National Center for Biotechnology Information), EMBL (European Molecular Biology Laboratory) and DDBJ (DNA Data Bank of Japan).

• Go to http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome
• You can choose the link "Viruses" to reveal the categories of known viral genomes. Find "Influenza Virus" and then go to "Sequences from the human A (H7N9) 2013 outbreak" link.
• A list of all submitted H7N9 segments of its DNA is revealed. By clicking on individual identifiers we reveal the sequences for corresponding gene of H7N9 virus.