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Xine v4 issue 1

Xine Volume 4 Issue 1

Dear Colleagues:

Welcome to Xine, the source for Xenopus news and information. Here’s what’s happening…


From Richard Harland:

The Joint Genome Institute has made available a preliminary assembly of the Xenopus tropicalis genome for blast searches.

http://genome.jgi-psf.org/xenopus0/xenopus0.home.html

They were hesitant to do this, since the coverage is still spotty, and the contig size relatively small, but at our last meeting in Washington there was very strong encouragement from our community to release an assembly. For some regions it will aid the community in exploiting this valuable resource.

In the meantime, sequencing is proceeding apace, and another report will be available shortly after February 10th at http://tropicalis.berkeley.edu/home/mission/genome_seq/genome.html


Following is a request for letters of support from Don Brown to encouerage sequencing of the Xenopus laevis genome, in addition to the sequencing of the Xenopus tropicalis genome. As you may know, letters of support are a particularly valuable mechanism for demonstrating the value of such proposals to the research community and strongly influence whether such proposals are funded or undertaken. There was relatively strong support expressed for at least a limited sequencing of the X. laevis genome at our last meeting in Washington on Xenopus genomics. If you would like to see X. laevis sequenced I encourage you to send letters or emails indicating your support to Don as described below.

Dear Colleagues:

I am writing an application to the JGI to convince them to sequence the Xenopus laevis genome. They have something called the "Community Sequencing Program" (http://www.jgi.doe.gov/) that reviews requests and chooses organisms for sequencing. The next deadline for an application is February 20. As you know, they are completing the X. tropicalis genome. Since the X. laevis genome is larger and pseudo tetraploid, they are unlikely to carry out the full 8 or so passes required for a complete assembly. However, they are sympathetic to three passes and perhaps willing to concentrate on specific requested regions. For success, this application will need broad community support. If I am to oversee this application I will need your input. Here is how you can help.

1. Send me a page or more of your reasoning that details why sequencing the X. laevis genome would be useful. Outline the scientific questions that having the sequence in hand will help. I will paste these letters together as part of the application.

2. Simply affirm your support. I suppose an e-mail (use email address at the bottom of this page) to this effect will do. I will submit a list of supporters.

3. This message is being sent to those of you on lists of previous Xenopus meetings so it is incomplete. Feel free to distribute this letter and urge others to contribute to this application.

I will collect everything and try to make the February 20 deadline.

Best regards,

Don

Donald D. Brown
Carnegie Institution
115 W. University Pkwy
Baltimore, MD 21210
e-mail: xenopus@ciwemb.edu


If you wish to read Xine in html format and/or see back issues, they are available at the following places

http://blumberg-lab.bio.uci.edu/xine/index.htm
http://blumberg-serv.bio.uci.edu/xine/index.htm
http://blumberg.bio.uci.edu/xine/index.htm
http://www.xenbase.org/xine/xine.html


Subscription information

I have constructed the Xine mailing list from serveral sources. As always, if you are not on the list and wish to be, want to update your e-mail address or would rather not receive it at all, please contact Bruce Blumberg (blumberg@uci.edu).

Until next time.

Bruce

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