AUGUSTUS + CanFam3

[Arumilli, Meharji]

Dear Receiver,

 

We are in need of the training parameters that have been used for ab initio gene predictions in Dog (canFam3) using AUGUSTUS. We could find the gene predictions in UCSC table browser but not the training parameters anywhere. Could you guide us to find the same.

 

Br

Mehar

 

Meharji Arumilli, MSc

PhD Candidate

Canine Genetics Research Group

University of Helsinki and 

The Folkhälsan Institute of Genetics

 

 

[Matthew Speir]

Hi Meharji,

Thank you for your question about the AUGUSTUS genes track for dog (canFam3) in the UCSC Genome Browser.

Please refer to the description page of the track for more information on how this track was created: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=canFam3&g=augustusGene. From the Genome Browser, you can get to the track description page by either clicking the gray bar to the left of the track in the display or you can click the track name in the track groups below. In the Table Browser, you can view the track description page by clicking the "describe table schema" schema button next to the table name.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To post to this group, send email to gen...@soe.ucsc.edu.
Visit this group at https://groups.google.com/a/soe.ucsc.edu/group/genome/.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/EB79E0AB-912B-42F8-8EB2-4B291FB7412A%40helsinki.fi.
For more options, visit https://groups.google.com/a/soe.ucsc.edu/d/optout.

[Arumilli, Meharji]

Dear Mathew,

 

Thank for your email. The "describe table schema" page shows that the “Human and all other vertebrates” assemblies have been trained using “human” as the training species.  If I understood it correct, “human” is used as training species for “dog” assembly as well? as no dog specific information is not documented?

 

Br

Mehar

 

 

 

From: Matthew Speir <msp...@soe.ucsc.edu>
Date: Monday, 26 June 2017 at 23.35
To: "Arumilli, Meharji" <meharji....@helsinki.fi>, "gen...@soe.ucsc.edu" <gen...@soe.ucsc.edu>
Subject: Re: [genome] AUGUSTUS + CanFam3

 

https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=canFam3&g=augustusGene

[Matthew Speir]

Hi Mehar,

Yes, this means that human was used as the training species when we ran AUGUSTUS on the canFam3 genome assembly.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group