Re: [genome-www] Requesting to incorporate the Watermelon genome database to UCSC genome databse

[Hiram Clawson]

Good Evening Fikru:

Can you find the assembly you refer to in this search form:


https://genome.ucsc.edu/assemblySearch.html?q=watermelon;browser=mayExist;maxItemsOutput=500

and use the 'request' function on your assembly of interest.

--Hiram

On 5/27/25 6:54 PM, Fikru Kenea wrote:
> Dear Sir/madam
> Greetings
>
> I am Fikru Tamiru from Zhengzhou Fruit Research Institute, CAAS, China. We
> are inspired to use genome database of UCSC website. But, our intended
> plant genome is not found in UCSC. Please, could you incorporate the Genome
> Database of "Watermelon (97103) genome V2" to UCSC genome database website.
> Thank you in advance for your assistance.
>
> *Thank you, *
>
> *Fikru Tamiru Kenea (PhD. candidate)WeChat ID: wxid_udaaonlgbz4a22*
> *Mobile cell phone:+8617501056544*
> *Institutional email: 2023Y9...@caas.cn <fik...@du.edu.et>*
> *Another Email Address: fikr1...@gmail.com <fikr1...@gmail.com>*
> 1. Graduate School of Chinese Academy of Agricultural Sciences, Beijing,
> China
> 2. Dilla University, Ethiopia

[Hiram Clawson]

Good Morning Fikru:

This genome assembly is a 'genbank' assembly. It does not have any
gene predictions on it. I do not see any 'RefSeq' assembly version
of this species which would have gene predictions:


https://www.ncbi.nlm.nih.gov/books/NBK50679/#RefSeqFAQ.what_is_the_difference_between_1

If you have protein sequence for a specific gene, you can blat that
protein to the genome to find the potential location of a gene
that is related to that protein.

The 'RefSeq mRNAs' track has all the RefSeq mRNA sequences mapped to
this genome, but there are no names associated with the mapped locations.

--Hiram

On 5/31/25 1:04 AM, Fikru Kenea wrote:
> Dear Prof. Hima,
>
> Thank you very much for your response. When I search for a specific gene, I
> cannot get it. Does it have another method to search for a gene?

>
>
> *Thank you, *
>
> *Fikru Tamiru Kenea (PhD. candidate)WeChat ID: wxid_udaaonlgbz4a22*
> *Mobile cell phone:+8617501056544*
> *Institutional email: 2023Y9...@caas.cn <fik...@du.edu.et>*
> *Another Email Address: fikr1...@gmail.com <fikr1...@gmail.com>*
> 1. Graduate School of Chinese Academy of Agricultural Sciences, Beijing,
> China
> 2. Dilla University, Ethiopia
>

[Maximilian Haeussler]

(Dropped Fikru)

This is a case where we added a GCA_ for which there are GCFs of the same organism. 

One day, we can give people excellent gene models by lifting the gene models from one of the watermelon GCF_xxxx assemblies to this assembly...

--

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