RE: GCA_001624865.1 BLAT

[Karn, Robert]

Thanks for contacting me, Luis. I found that if I use “spretus” as a query to try to access the Mus spretus genome, it will not let me do that. However, if I use “Algerian mouse” it takes me to western wild mouse 26 Apr 2016/SPRET_EiJ_v1 (SPRET_EiJ) and from there I can get Mus spretus genomic DNA (“>hub_158535_SPRET_EiJ_dna . . . ”). I can also access that DNA using “western wild mouse” on the genome home page. So, although it indicates that I will access the Mus spretus genome using the “spretus” query, it really won’t.

Bob Karn

 

 

From: Luis Nassar <lrna...@ucsc.edu>
Sent: Tuesday, November 1, 2022 12:22 PM
To: genome-www list <genom...@soe.ucsc.edu>; Karn, Robert <rk...@butler.edu>
Subject: GCA_001624865.1 BLAT

 

Hello, Bob.

I'm writing to you back on behalf of the UCSC Genome Browser regarding your question about BLAT on GCA_001624865.1.

We are not currently seeing any issues with BLAT or extracting DNA on GCA_001624865.1. Sometimes the BLAT servers can have momentary problems, but we wanted to confirm that everything is working on your end as well.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

[Karn, Robert]

Thanks for this, Max. I recently exchanged email with a researcher in Diethard Tautz’ lab regarding work they have been doing on the Mus spicilegus genome. He said that they had recently submitted an updated version of that genome to NCBI. I checked this by BLASTing a mouse genome version of a sequence to (organism) Mus spicilegus but BLASTn only retrieved a partial sequence we submitted 20 years ago.

 

My question is this: Does the UCSC browser team have any information on genomes for either M. spicilegus or M. macedonicus. They are two very important Mus species that would enhance studies of the Mus lineage such as those we have studied (see attached paper).

 

Thanks,

Bob Karn

 

From: Maximilian Haeussler <mhae...@ucsc.edu>
Sent: Thursday, November 3, 2022 8:28 PM
To: Karn, Robert <rk...@butler.edu>
Subject: Re: [genome] RE: GCA_001624865.1 BLAT

 

Hi Bob,

You found a bug. Thanks for this email! We'll fix this soon. In the meantime, my colleagues mention a few ways to work around it.

 

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[Luis Nassar]

Hi Bob,

Regarding those mus genomes, I see the following M. spicilegus genome on genbank (https://www.ncbi.nlm.nih.gov/assembly/GCA_003336285.1) is that the one you are referring to? We can request that on our assembly request page (https://genome.ucsc.edu/assemblyRequest.html) and it should be available in a few days.

I was not able to find any assembly for M. macedonicus, however. We do have a requirement that any browsers we build first be deposited into genbank, and our pipeline is largely built to ingest from there.

If you have a link or GCA/GCF accession to any genomes we can get browsers set up for them.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/BYAPR05MB431043B1B1A8C06FAE074B57DC3B9%40BYAPR05MB4310.namprd05.prod.outlook.com.

[Karn, Robert]

That would be super, Lou. I don’t think it’s the one my friend at Max Planck in Plön referred to because I see that it is attributed to Oklahoma State University, but I would certainly use it, especially if I an use the BLAT tool to explore it.

[Luis Nassar]

Hey Bob,

I figured that wasn't the one when I saw the Oklahoma State, but it was worth asking. Sounds good, though. You should have received a message that the new browser will be built soon. Typically they take a few days and once ready will have BLAT support.

Do let us know if you would like to explore any other genomes that have been deposited to NCBI.

Lou Nassar
UCSC Genomics Institute