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Three Armadilloes in captivity - they are natural hosts of Mycobacterium leprae
Armadilloes - natural hosts of Mycobacterium leprae

Exploring pseudogenes in Mycobacterium leprae

In this Step you will explore 5 different pseudogenes across the Mycobacterium leprae genome, you will investigate their annotation and make comments on their GC content.

Previously we described just one pseudogene out of a possible 1,000 pseudogenes in M. leprae. Thankfully this is a well-annotated genome and most pseudogenes should be annotated as such.

Your first task is to scroll along the genome and select five pseudogenes. Confirm that they are indeed pseudogenes by checking their annotation and also visually inspecting that they have at least one premature stop codon.

Once you have identified your pseudogenes:

  • Write down the locus_id and any other useful information provided, such as an ortholog gene in another species and its putative function.

For each pseudogene find the GC content (or GC%):

  • Use the View menu, select “Feature Statistics”

  • You will then need to use the sequence in a BLAST (Hint: use blastx search) search to confirm the predicted functional annotation and also to confirm that the same has not been updated or changed since the genome was published.

  • Lastly, check the functional annotation in the Mycobacterium tuberculosis genome file and note down the function of its ortholog gene, if indicated in the M. leprae annotation.

Keep this information because you will need it for the next Step.

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This article is from the free online course:

Bacterial Genomes II: Accessing and Analysing Microbial Genome Data with Artemis

Wellcome Genome Campus Advanced Courses and Scientific Conferences