Getting the nucleotide and amino acid sequences.

Sometimes it is useful to extract the sequence of our gene or protein of interest from Artemis. Here you will learn how to do just that!

In order to extract the nucleotide sequence of a given gene you need to simply follow these steps. Click on the gene that you are interested in and make sure it is highlighted, you should see its borders in bold and its annotation in the bottom panel is also highlighted. Click on the ‘View’ menu and you will see various options including two that state ‘Bases’ and ‘Amino Acids’. Each of these selections will have options for viewing the bases or amino acids in different formats.

Explore the different formats and decide which one would be more appropriate to use in a similarity search (i.e. BLAST search) on an external database.

In addition to this functionality, it is also possible to save the sequence information to files. To do this, select one of the features (gene, CDS or any other), go to ‘File’ and select ‘Write’. Here you will be presented with a number of options including ‘Amino acids of selection’ and ‘Bases of selection’. The latter also includes different file formats to save the sequence data. Explore these options by choosing different options for file format within the ‘Bases of selection’ and compare them. In which scenarios do you think you will need the different formats?

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This article is from the free online course:

Bacterial Genomes: Accessing and Analysing Microbial Genome Data

Wellcome Genome Campus Advanced Courses and Scientific Conferences