Download Exercise 1

Workshop on Bacterial Genomics
Module 1: Artemis
Artemis Exercise 2
This exercise will look at a section of the Malaria genome. You will need to close down
the last Artemis exercise if you haven’t already done so. Then start a new Artemis
Session, as before, using the file ‘Malaria.embl’ in the current directory
(Module_2_Artemis). Unlike the Salmonella exercise, in this instance the annotation and
sequence are contained within the same file ‘Malaria.embl’
The sequence you are going to look at is a small region of contrived sequence (~21 kb)
taken from Plasmodium falciparum chromosome 13. You will see 7 CDSs, some with
multiple exons. As a gentle introduction to splicing we would like you to look at the
genes named , PF13_0119, MAL13P1.294 and PF13_0061. They have only been
partially characterised and may in fact be missing exons. Have a look at these CDSs and
confirm, edit or dismiss the proposed gene models by using G+C content, database
searches and looking for splice sites (Appendix IX).
G+C content is a very good indicator of coding capacity in Malaria. On average, the
coding regions are ~23% G+C and the non-coding regions are ~19%. Have a look at the
G+C content for this region by selecting the appropriate graph. Left click within the
graph window and then select by clicking on the exons to see how this relates to the
G+C peaks on the graph.
Note, we will cover the principals and methods of gene prediction in much more
detail in a module 3.
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