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Old 11-04-2012, 07:49 PM   #1
Bgansw
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Location: Sydney, Australia

Join Date: Nov 2011
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Default 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
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Old 11-04-2012, 08:58 PM   #2
zhaowei
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You could download annotation from NCBI, if you just want to use it. ftp://ftp.ncbi.nih.gov/genomes/Fungi/
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Old 11-05-2012, 01:06 AM   #3
Apexy
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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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