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Xine Volume 4 issue 3

Xine Volume 4 issue 3 - June 2004

Dear Colleagues:

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

REMINDER - 10th International Xenopus Meeting - 2004

The application deadline, July 1, is fast approaching.

Where: Marine Biology Laboratory Woods Hole, MA
When: September 14-18, 2004
How: Register for the meeting at
http://www.mbl.edu/xenopus

The International Xenopus Meeting is held every two years and is
the only meeting that brings together, from around the world,
researchers using Xenopus as a model system. This meeting will
include sessions on a wide variety of subjects, including: the Cell
Cycle, the Cytoskeleton, Oogenesis and Gametogenesis, Early
Development, Organogenesis, Emerging Technologies and
Genomics. There will be platform presentations, posters and ample
time for informal interactions. Marc Kirschner (Harvard Medical School)
will present this year’s plenary lecture.

Please register early, and include an abstract if you wish to present a
poster or platform presentation.

Xenopus tropicalis genome project - Assembly v2.0 now available!

X. tropicalis genome assembly 2.0 is the second of a series of preliminary assembly releases that are planned as part of the ongoing X. tropicalis genome project. Sequence is accumulating and users should expect steady improvements in the quality and length of assembled contigs and scaffolds in future releases. The current assembly includes approximately 4.7X in small insert end-sequence coverage (see below for details). A higher quality draft genome sequence based on ~ 6X shotgun depth is expected sometime in the summer of 2004. The quality of this assembly will determine the extent of additional sequencing that will occur through the end of 2004. A final draft assembly based on ~8X sequence coverage and incorporating other data including bac-end sequences and physical map information will be complete in the first half of 2005.

Our goal is to make the genome sequence of Xenopus widely and rapidly available to the scientific community. We endorse the principles for the distribution and use of large scale sequencing data adopted by the larger genome sequencing community and urge users of this data to follow them. It is our intention to publish the work of this project in a timely fashion and we welcome collaborative interaction on the project and analyses.

Questions concerning this project or the use of these data should be sent to Paul Richardson (PMRichardson@lbl.gov).

Paul Richardson, on behalf of the X. tropicalis Genome Consortium

    Editor's note:

Users of the X. tropicalis genome assembly should be aware that this is an early stage assembly that has been provided for the benefit of the community in advance of the "finished" release. Please keep this in mind when using the sequence and appreciate the assembly for the utility it has, rather than complaining because it is not yet perfect (as has happened already with version 1.0).

Xenopus tropicalis full-length gene collection now available

We would like to announce the launch of a publicly available database (http://informatics.welc.cam.ac.uk/online/xt-fl-db.htm) containing the identification of a large set of full-length clones from a Xenopus tropicalis EST project done in collaboration with the Sanger Institute.

The data and methods used in constructing the database are described in: Gilchrist, M., Zorn, A. M., Voigt, J, Smith, J.C., Papalopulu, N. and Amaya, E. (2004). Defining a large set of full length clones from a Xenopus tropicalis EST project. Dev. Biol. in press

The primary purpose of this database is to accelerate the process of gene discovery and function in Xenopus. Clones can be obtained from the MRC Geneservice ( http://www.hgmp.mrc.ac.uk/geneservice/reagents/products/descriptions/XtropEST.shtml ).

Mike Gilchirst, Nancy Papalopulu and Enrique Amaya

Information on X. tropicalis EST sequences from the Sanger Centre

Dear X. tropicalis EST users,

The Sanger EST sequencing and analysis teams are pleased to announce the availability of updated fasta files on the X. tropicalis FTP site:

ftp://ftp.sanger.ac.uk/pub/EST_data/Xenopus/LATEST_ESTs/

Please see ftp://ftp.sanger.ac.uk/pub/EST_data/Xenopus/LATEST_ESTs/README for the site notes

Email queries to: estdb@sanger.ac.uk, trop@sanger.ac.uk

best regards,

The Sanger Centre Team

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
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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