What programs can be used to predict all of the coding sequences in a eukaryotic genome?
I am interested in generating a gene set from a eukaryotic genome assembly and am interested in knowing what my options are for extracting genes. I've heard there are programs that can make predictions based on regions upstream of the gene, and even to predict introns.
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Eukaryotic genome annotation steps
https://en.wikipedia.org/wiki/List_of_gene_prediction_software
EDIT:
I don't want to offend you but I think that putting your question in google is much faster then creating a post here. Is it possible that we misunderstood your question and you need to know more details or something?
I was hoping that people could give more details or recommendations, but people have given some helpful links so far.
The lack of details reflects the lack of information we have. There are different tools and approaches one can use depending on available data.
Comprehensive list of tools here.
To understand the different approaches have a look a this course: Methods in genome annotation
Adding the Ensembl gene annotation pipeline to the list (paper).