Question: Methods of annotating a genome?
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gravatar for jamie.pike
11 weeks ago by
jamie.pike20
jamie.pike20 wrote:

Hello,

I have some fungal genomes that I downloaded from NCBI, it appears that 5 of the genomes have not been annotated. I have a set of Blast hits, and I want to see if I can match the locations of the hits to see if they overlap with any gene models. Initially, I tried uploading the genomes to fgenesh, as I have no experience annotating genomes. However, fgenesh just produced an error message (I think the files were too big).

I have since tried to use maker, but I'm having trouble with it. Are there any alternatives to fgenesh online that can handle larger files (~ 49MB)? Is there a way of using maker that produces annotations to a similar standard without it taking days? I understand that maker can be run and trained using SNAP, AUGUSTUS etc, but I'm not sure that is necessary and I think it will end up taking me forever, as I don't really understand the process.

Any advice would be much appreciated

Cheers, Jamie

ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by jamie.pike20

I am going to hazard a guess that you are interested in some specific gene(s) in these genomes? Is that correct? If so it may be much simpler to go after those rather than try to annotate the entire genome (which is not a trivial undertaking).

ADD REPLYlink written 11 weeks ago by genomax85k

Kinda, I have a transposable element which is often found in the promoter region of effectors, so I want to use that to see if I can identify so new putative effectors. The problem is I have roughly 100 hits per genome, so any manual annotating the specific regions may take a while too? A lot of the hits are one the same contigs, do you think it's worth trying to upload just the contigs to somewhere like fgenesh?

ADD REPLYlink written 11 weeks ago by jamie.pike20

do you think it's worth trying to upload just the contigs to somewhere like fgenesh?

Sure. If you know that the region your are interested in is located there.

ADD REPLYlink written 11 weeks ago by genomax85k
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