Denovo genome assembly annotation

Question

[1234anjalianjali1234]

Hellow,

I am currently using the PacBio portal for the purpose of denovo genome assembly of a fungal genome. Now, I have assembled genome and wanted to explore and annotate it. Could someone guide me to go further I am new to this... Thankyou

Answer 1

[Juke34]

Here are described the best approaches:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207268/

Using Genemark alone probably will give you a first good draft of your annotation. In most of case it would be enough. It depends what you plan to do next. Genemark with proteins (Gnemark-P) or ESTs (Genemark-ET) will provide you an annotation even better.

[1234anjalianjali1234]

Thankyou Juke, I already read that paper but my problem is to run Genemark-ES ... Could you provide me with some useful tutorial regarding Genmark...

[Juke34]

I don t have any tutorial. It should be pretty straightforward to use. Have you tried to launch it at least ? Have you read the readme or/and the help ?

If you run into problems we will be happy to help you.

[1234anjalianjali1234]

thankyou sir, I'll let you know.

[Juke34]

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[1234anjalianjali1234]

Sorry Juke, for the late reply,

Done using FunGAP pipeline.

Thankyou