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zebra fish reference sequences

asked 2013-10-03 16:52:38 -0700

We Liu gravatar image

Hi,

Is zebra fish genome sequences downloadable yet?

Thanks, Wei

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answered 2014-04-21 10:53:54 -0700

GenomeBrowse 2.0 has been released! You can download the most recent installer from our website.

Included in this new version is support for several new species as well as new genome builds for existing species. Both the Zebrafish (Danio rerio, Zv9) and Mosquito (Anopheles gambiae S Pimperena, AgamS1) genomes are now supported and can be selected from the genome selection drop-down menu.

Thanks, Jami...

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answered 2013-12-04 16:46:33 -0700

Hi Mark,

I have added your genome to the list of genomes to be made available. Thank you for providing a link to the data, I will let you know as soon as it becomes available.

For visualizing the genome in GenomeBrowse we need to create an assembly file for the species, this is basically just a list of the assembled chromosome names (or scaffold names) and their corresponding lengths. Do you know a good source for a listing of the scaffold lengths? I found a listing of the scaffold names from the NCBI website at the following link. If you aligned a BAM file to this genome the header of your BAM file would contain this information.

Let me know if you have any further questions.

Thanks, Jami...

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answered 2013-12-01 10:16:59 -0700

I'm interested in adding the reference genome of Anopheles gambiae (mosquito) Pimperena.

https://www.vectorbase.org/organisms/anopheles-gambiae/pimperena-s-form

Any chance?

Thanks, Mark B.

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answered 2013-10-04 09:45:46 -0700

Dear Wei,

Thank you for your question.

We are in the process of updating our available genomes and I will add the zebra fish genome to the list. Do you have a particular version release of the genome that you would like included? If not then I will just add the build Zv9 to the list.

Our list of tracks to be updated/created is quite large so it may be a while before the tracks become available.

Please let me know if you have any further questions.

Thanks, Jami...

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Asked: 2013-10-03 16:52:38 -0700

Seen: 107 times

Last updated: Apr 21 '14