annotating large number of eukaryotic contigs

[fznajar]

What is the best way to annotate large number of contains from a eukaryote. BlastX is going to take a long time. I was wondering if FgeneSH will be a better first step?

[WhatsOEver]

What is it exactly that you want to do?
It sounds like you want to gene prediction and annotation in one run which doesn't work.

Do gene prediction first (here is a small list of programs http://en.wikipedia.org/wiki/List_of...ction_software). For eukaryotes I prefer augustus or genemark.

For gene annotation you can use something like Blast2GO which is very easy to use. But it takes some time...

[lkral]

Fgenesh worked very well for my needs as a first step to identify potential genes. To actually annotate, fgenesh++ would be needed but I have not been able to try that out with my scaffolds (anyone have any experience with this program?) My workflow is to import the fgenesh results into webapollo and then do the rest of the annotation steps manually:

http://www.westga.edu/~lkral/poster/PAG-poster.pdf

[fznajar]

I was worried that since its eukaryote, there would be few full length genes on each contig.

appreciate both of you.

Best,

[lkral]

Depends how long the contigs are. It is likely that even long contigs (over 10 Kb) will contain only partial genes. But as long as you are not trying to carry out whole genome comparisons you can assemble whole genes of interest from the partial genes in these contigs (as long as these are single copy genes).