Question: Annotation of non model fish (mahi mahi) genome
0
gravatar for kspata
3 months ago by
kspata70
Chicago
kspata70 wrote:

Hi,

I have an assembled genome obtained from oxford nanopore reads. How can I perform a basic annotation to obtain a genbank file? What tools are available to perform eukaryotic genome annotation.

I had previously used RAST for bacterial genome annotations, can I use this tool for eukaryotic genoem annotation as well?

Thanks in advance !!

annotation assembly • 157 views
ADD COMMENTlink modified 3 months ago by Shalu Jhanwar470 • written 3 months ago by kspata70
1

Take a look at MAKER. If you have a transcriptome available then: GAWN - Genome Annotation Without Nightmares

ADD REPLYlink modified 3 months ago • written 3 months ago by genomax91k

Afaik, you cannot use RAST because it doesn't support eukaryote gene models and uses only homology within bacteria as evidence.

ADD REPLYlink written 3 months ago by Michael Dondrup47k

Have you polished the genome extensively (eg with medaka, racon?). Else your annotation will suffer from false frameshifts in reading frames due to indel errors. Even after polishing this is a big problem.

ADD REPLYlink written 12 weeks ago by colindaven2.4k
0
gravatar for Shalu Jhanwar
3 months ago by
Shalu Jhanwar470
Switzerland
Shalu Jhanwar470 wrote:

There are different genome annotation tools available. Have a looks at below resources to get the most comprehensive and widely accepted tools:

https://www.1010genome.com/eukaryotic-genome-annotation/

https://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/

https://www.gensas.org/

ADD COMMENTlink written 3 months ago by Shalu Jhanwar470
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