Question: Don't understand the assignment - Artemis
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gravatar for Mimmi Ahlmén
20 months ago by
Mimmi Ahlmén20 wrote:

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?

artemis • 406 views
ADD COMMENTlink modified 20 months ago by lexa.matej20 • written 20 months ago by Mimmi Ahlmén20
1

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

ADD REPLYlink written 20 months ago by lieven.sterck7.9k

Did you try asking your Professor/TA?

ADD REPLYlink written 20 months ago by RamRS27k

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

ADD REPLYlink written 20 months ago by 5heikki8.9k
1
gravatar for lexa.matej
20 months ago by
lexa.matej20
lexa.matej20 wrote:

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

ADD COMMENTlink written 20 months ago by lexa.matej20
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