Don't understand the assignment - Artemis

Question

[Mimmi Ahlmén]

I am currently doing an assignment were I have the genome of a prokaryote.

In this assignment you will compare two methods of finding putative genes and evaluate their results. You will then further analyze the coding sequences by doing promoter predictions and comparing all the results. Use the naive ORF finding tool (getorf) and the combined approach tool (GeneMarkS) as outlined in the gene identification tools section. Compare both methods preferably using Artemis.

I used ORF finding tool and GeneMarkS so now I have two separate orf files to compare. Now I want to use Artemis but I don't get it. I have one genome, shouldn't I have something to compare it with, I mean isn't that the thing with Artemis?

[lieven.sterck]

opening both prediction result in Artemis will allow you to compare the result manually. Each annotation goes in a different 'track' and then you can just browse over the sequence and see what the differences are. (as lexa.matej says, you will compare two gene prediction results for the same genome, so you only need one genomic sequence)

For a more global picture of the comparison I would go in script-wise to calculate stats etc

[Ram]

Did you try asking your Professor/TA?

[5heikki]

Perhaps you're supposed to compare the ORF annotations, percent that intersect, percent unique to either method, etc.

Answer 1

[lexa.matej]

I'd say you'll be comparing two annotations of the same genome against each other.