How long does it take to assemble, annotate and predict secondary metabolites?

Question

[Andrés Medel]

Hello everyone. This is my firt post here. I have just known about this site a few weeks ago.

I am into planing my thesis on a master degree and I have never worked before with bioinformatics. What i will do is to predict some secondary metabolites after sequencing the hole genome of three bacterias.

I am wondering (based on your eperience) how much time may it take to me doing so. I have identified at least three steps: assembly, make annotations and predict the secondary metabolites. Consider that I am TOTALLY new on this.

I read you all. Thanks.

Answer 1

[GenoMax]

If you have the data and access to correct hardware then assembly part should not take more than a couple of days. You could use a program line prokka (LINK) to do basic genome annotation. Then it would be a matter of using secondary metabolite prediction tools (LINK).

Much of this will depend on quality of your input sequence data. If that is not very good then no amount of informatics can turn it into results.

[Andrés Medel]

Thank you.