Fungal genome Annotation

Bgansw · 11-04-2012, 07:49 PM

Hello,

I'm new to genome assembly.

I've got fungal genome, that I've assembled using Velvet and Soap denovo. I have used Genemark for gene calling. Now how do I annotate it?

Are there any webtools available for fungal genome assembly, or would I have to use a linux based software?

Any help would be soo sooo appreciated!

Thanx

bgansw

zhaowei · 11-04-2012, 08:58 PM

You could download annotation from NCBI, if you just want to use it. ftp://ftp.ncbi.nih.gov/genomes/Fungi/

Apexy · 11-05-2012, 01:06 AM

Hi,

You could try out AUGUSTUS http://augustus.gobics.de/ . It has been extensively tested on fungal sequences and there are quiet of good number of training sets from fungi in the package. It also enables you to use RNA-Seq data should you have one. The annotations as suggested by zhaowei such as related proteomes can also for used to constrain the prediction.

HTH

Enjoy!

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11-04-2012, 07:49 PM	#1
Bgansw Member Location: Sydney, Australia Join Date: Nov 2011 Posts: 24	Fungal genome Annotation Hello, I'm new to genome assembly. I've got fungal genome, that I've assembled using Velvet and Soap denovo. I have used Genemark for gene calling. Now how do I annotate it? Are there any webtools available for fungal genome assembly, or would I have to use a linux based software? Any help would be soo sooo appreciated! Thanx bgansw

11-04-2012, 08:58 PM	#2
zhaowei Junior Member Location: oh Join Date: Jan 2011 Posts: 9	You could download annotation from NCBI, if you just want to use it. ftp://ftp.ncbi.nih.gov/genomes/Fungi/

11-05-2012, 01:06 AM	#3
Apexy Member Location: Africa Join Date: Apr 2011 Posts: 62	Hi, You could try out AUGUSTUS http://augustus.gobics.de/ . It has been extensively tested on fungal sequences and there are quiet of good number of training sets from fungi in the package. It also enables you to use RNA-Seq data should you have one. The annotations as suggested by zhaowei such as related proteomes can also for used to constrain the prediction. HTH Enjoy!