A general method and good student project for finding interesting anomalies in GenBank

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Sandra Porter

Do mosquitoes get the mumps? Part V. A general method for finding interesting things in GenBank

This is the last in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes and a general method for finding other interesting things.

In this last part, I discuss a general method for finding novel things in GenBank and how this kind of project could be a good sort of discovery, inquiry-based project for biology, microbiology, or bioinformatics students.

I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III. Serendipity strikes when we Blink.
IV. Assembling the details of the case for a mosquito paramyxovirus
V. A general method for finding interesting things in GenBank

A general method for finding interesting things in GenBank

*Note: I'm including the first two steps for reference. If you like, you can go straight to the links in step 3 and find the viruses. If you want to see how this method works, take a look at the other parts in this series and see how I found a gene from a paramxyovirus in a mosquito genome

1. We begin by going to the NCBI.

2. Use either one of these two paths to get to the Entrez Genomes Home page.

  • Select Genome from the pull-down menu on the home page and click the Go button.
  • Click the Go button on the home page and click the link to the Genome database.

3. Look on the left side of the page for Viruses. Click either Viruses, Phage, or Viroids.

  • Viruses: takes you to a list of at least 2652 genome sequences for viruses that infect eucaryotes.
  • Phage, you go to a list of at least 500 viruses that infect bacteria.
  • Viroids - you'll a list of 39 viroid sequences.

I suggest using viruses, phage, or viroids because their genomes are small, they generally match other viral sequences best, and it's not too daunting to look at less than 10 proteins in sufficient detail.

4. Select the Accession number link to get to the genome sequence. Note - some viruses, like influenza, have genomes that consist of physically separate pieces. For those viruses, you may need to look at each piece.

5. You should now be at a page with a table that contains information about the viral genome. Scroll to the very bottom of the page and look for the link to the Sequence Viewer and click it.

6. Mouse over the red bars that represent protein sequences and use Blink to examine the blast results for each protein in the genome, one by one, just as I did here.

The cool thing about Blink is that shows the blast results grouped by the type of organism. This is very helpful for finding needles in haystacks.

7. Examine the Blink results and investigate any matches that are not viruses. Some of these matches will actually be to viral proteins that are in the wrong database, some will be to undiscovered viruses, and some, well, who knows what we'll find.

Have fun!