Yeast Genome Annotation

Question

[piearoo]

Hi everyone,

I am a bioinformatics student and currently having a genome annotation task which I don't know how to approach therefore I need your help.

I have to annotate yeast genome S. japonicus and I have the following files:

1. Contigs file (fasta) for the mentioned yeast.
2. Predicted coding sequences and proteins (fasta format each) using Augustus software where S. pombe was model species.
3. gff file for predicted genes.

I think that half of the job has been done by the prediction but I still have no clue how to annotate the genome.

Thanks in advance,

Pierre

Answer 1

[lieven.sterck]

if you ran Augustus (S pombe model) on your specific species then you might be done. Unless you need anything else? If you really need (want to) take it one step further you can create a S japonicus specific model with Augustus and run that on your fasta contig files.

what do you mean with 'annotate' : predict genes or also assign potential functions to them?

[piearoo]

Thanks Lieven, my bad you are right the annotation is already done. It was a misunderstanding since I'm
newbie in bioinformatics.

Cheers, Pierre