Exercise 3: Searching Genbank for further sequences and papers from the same species

Click on NCBI/Nucleotide (located in the Sources panel on the left) and search for additional sequences from Raphus cucullatus.


The results contained in the NCBI search folders are only temporary and will be deleted when you run a new search or close Geneious Prime. To add the sequences to your database, you must drag and drop them from the search folders to one of your Local folders in the Sources panel.

Select the cytochrome B sequence and then click on the Text View tab above the sequence viewer (this changes the view to the text Genbank record).

Under the text view tab you will notice a publication is listed - this is the original paper that described this Genbank sequence. You can read it by clicking here and clicking View Document.

The authors of this paper deposited the sequence on Genbank. When you publish a DNA sequence it is a requirement to deposit the DNA sequences onto Genbank so that other researchers can access them. Read the first paragraph of the paper - it will give you a little perspective on why researchers conducted this research.

Now click on NCBI/Pubmed (located in the left hand Sources panel) and search for the name of the first author of the Dodo paper (Beth Shapiro) to see what other papers she has published.

Pubmed is one of many online databases that records literature published in scientific journals. The results returned in Geneious Prime give a link to the abstract of the publication on the journal website, as well as a Google Scholar link which may show other copies of the paper.

To download articles from the NCBI/Pubmed search in a format that can be read by the Endnote citation software, select the papers you want and go to File → Export → Selected Documents, choosing "Endnote" as the format. To get a format that can be read by other citation software packages including Latex, click the Bibtex tab above the sequence view, and copy and paste the contents of the viewer into a text file.


Exercise 4: Genome searching