Question

Denovo genome assembly annotation

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6.4 years ago

1234anjalianjali1234 ▴ 50

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

genome sequencing denovo next-gen annotation • 2.2k views

ADD COMMENT • link updated 6.4 years ago by Juke34 8.5k • written 6.4 years ago by 1234anjalianjali1234 ▴ 50

score 0 · Answer 1 · 2017-12-13

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6.4 years ago

Juke34 8.5k

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.

ADD COMMENT • link 6.4 years ago by Juke34 8.5k

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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...

ADD REPLY • link 6.4 years ago by 1234anjalianjali1234 ▴ 50

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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.

ADD REPLY • link 6.4 years ago by Juke34 8.5k

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thankyou sir, I'll let you know.

ADD REPLY • link 6.3 years ago by 1234anjalianjali1234 ▴ 50

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ADD REPLY • link 6.4 years ago by Juke34 8.5k

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Sorry Juke, for the late reply,

Done using FunGAP pipeline.

Thankyou

ADD REPLY • link 3.7 years ago by 1234anjalianjali1234 ▴ 50