Prediction of genes and functions without reference genome

Question

[biobiu]

Hi, I plan to sequence the genome of un-referenced bacteria. My first goal is to try to define functional elements in the genome and next to predict their function.

My general idea is to assemble the reads into contigs, perform ORF calling, blast genes against DBs, translate the genes into proteins and look for conserved domains.

Any other idea? Assuming you will know the proteins sequence how would you predict its function?

[Joe]

Just use a tried and tested annotation pipeline like Prokka.

That pretty much does everything you describe and more

Answer 1

[proteina.cbe]

You can use PATRIC https://patricbrc.org/ in order to find interesting features of your new genome assembly.