Making a genome alignment between dm3 and the updated D. simulans genome

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Zhenguo Zhang

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Apr 22, 2016, 11:39:15 AM4/22/16
to gen...@soe.ucsc.edu
Dear UCSC Team:

My research now is using the genome alignments from your website, which are very helpful. Thank you for having made them.

Since D. simulans has gotten much better updated genome sequence (see the description and relevant links at http://flybase.org/static_pages/feature/previous/articles/2015_02/Dsim_r2.01.html) and most people in the Drosophila community may use the updated genome, it will be fantastic if a new genome alignment between dm3 (D. melanogaster) and the updated D. simulans genome can be made. Could you please make this genome alignment or do you have plan to make it?  Thanks.

Best regards!

Zhenguo
--

Zhenguo Zhang, Ph.D
University of Rochester
Department of Biology
River Campus Box 270211
Rochester, New York 14627-0211
Phone: (585) 276-2183;

Email: z.z...@rochester.edu or zhang...@gmail.com

Home Page: http://molevol.altervista.org/
Lab page: http://blogs.rochester.edu/PresgravesLab/

Cath Tyner

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Apr 22, 2016, 7:37:37 PM4/22/16
to Zhenguo Zhang, gen...@soe.ucsc.edu
Hello Zhenguo,

Thank you for using the UCSC Genome Browser and for submitting your question regarding a genome alignment among D. simulans (Dsim_r2.01) and D. melanogaster (dm3).

Since D. simulans (Dsim_r2.01) does not yet exist as a genome assembly in our browser, we do not have alignments to D. melanogaster (dm3). It is likely that we will have these data in the future - though completion time for the updated D. simulans assembly is currently unknown.

Until then, you can follow this "Whole Genome Alignment" wiki page and create your own liftOver files to convert annotations.

You can also search "Whole_genome_alignment_howto" in our Genome Browser forum archive for related information.

As you may already know, we do have alignments among droSim1 (D. simulans, Apr. 2005) and dm3 (D. melanogaster, BDGP Release 5, April 2006):

From the droSim1 gateway page, under the "Assembly details" section: http://genome.ucsc.edu/cgi-bin/hgGateway?db=droSim1
there are links to the following 2 locations where you can find alignment files:


2.1. From the link, D. simulans/D. melanogaster (dm3): http://hgdownload.cse.ucsc.edu/goldenPath/droSim1/vsDm3/

We have a work in progress - an automated Invertebrates Assembly Hub. This hub pulls data from Genbank genome assemblies. If you search the Invertebrates Assembly Hub for accession "GCA_000754195.2" (19 Sep 2014, Dsim R2.01, Drosophila simulans) you will find a link in the 3rd column, "common name" which will load this prototype hub:

GCA_000754195.2 (19 Sep 2014, Dsim R2.01, Drosophila simulans prototype hub

Please note the section on the hub's description page, "Download files for this assembly hub" for instructions using the wget command.

Thank you again for your inquiry and for using the UCSC Genome Browser. 
​Please send new and follow-up questions to one of our UCSC Genome Browser mailing lists below:

  * Post to the Public Help Forum: E
mail 
gen...@soe.ucsc.edu
​ or search the Public Archives
​  * Post to the Mirror Help Forum: Email
 
genome...@soe.ucsc.edu 
or search the Mirror Archives​
​  * Confidential/private data help: Email
 
genom...@soe.ucsc.edu

​Enjoy,​

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