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Xine Volume 3 Issue 1

Xine Volume 3 Issue 1

Dear Colleagues:

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

Xenopus tropicalis BAC filters

As you know, the Department of Energy Joint Genome Institute is undertaking to sequence the entire trop genome. As part of this effort, several BAC (Bacterial Artificial Chromosome) libraries have been created through an NIH initiative. In addition to the use of these BACs for large-scale sequencing and mapping, there is considerable interest in identifying a set of BACs from regions of strong biological interest. Since one of the justifications for sequencing the X. tropicalis genome is to facilitate comparative genomic analysis, it makes a lot of sense to prioritize the sequencing of regions that will advance this objective. These will be assigned a high priority for full sequence determination.

JGI needs community support to identify such a set of prioritized BACs. Specifically what is needed are labs who are willing to screen the library filters with their favorite probes to identify the corresponding BAC clones. In turn, these will be prioritized and those of the greatest interest selected for sequence determination. The draft sequence data will be made available on the JGI website immediately upon sequencing as ordered and oriented contigs.  These BACs will then be finished by JGI and updated on the web as finished sequence becomes available.

The Xenopus tropicalis libraries and filters are available through CHORI (Children’s Hospital Oakland Research Institute).  Investigators should arrange to receive filters and clones through CHORI (http://www.chori.org/bacpac/).  In addition, the JGI has a limited capacity to screen filters with specific sequences.   An application for filter screening and sequencing of specific BACs will soon be available on the JGI web site

http://genome.jgi-psf.org/xenopus1/xenopus1.home.html

Applications for sequencing will be reviewed and prioritized by the Xenopus tropicalis genome project Advisory Board.
See http://genome.jgi-psf.org/xenopus1/X.tropicalis_board.doc for more information about the Advisory Board.

The application will ask for  the following information:

1.      A statement of how many genes the laboratory has an interest in and the time frame in which screening will be completed.

2.      A brief justification for DOE purposes stating why these genes are of biological interest and should be prioritized.

Regions that advance comparative genomics, particularly those that exploit the phylogenetic position of Xenopus will receive the highest priority.
Status of each application will be posted on the web site, and sequence will be made available immediately upon assembly and draft sequence verification.

X. tropicalis genomic BLAST server online

A BLAST server is now online for comparisons with the emerging Xenopus tropicalis genomic sequence. You can access the DOE-JGI Xenopus web site here

http://genome.jgi-psf.org/xenopus1/xenopus1.home.html

And the BLAST server directly here

http://aluminum.jgi-psf.org/prod/bin/runBlast.pl?db=xenopus1

Newly updated Xenopus clearinghouse web site.

Steve Klein has recently updated the NIH Xenopus web site to make it more useful to the community. You can access it here

http://www.nih.gov/science/models/xenopus/resources/index.html

Input solicited for new edition of Xenopus Laboratory Manual

Hazel Sive, Richard Harland and Rob Grainger are planning a new edition of the Xenopus laboratory manual (Early Development of Xenopus: a course manual; published by Cold Spring Harbor Laboratory Press). Input from the community would be of considerable value in developing this new edition. Therefore, they would like to have any and all comments regarding the manual in order to improve the new edition. The following questions are of particular interest:

1.      What mistakes did you find in the first version of the manual

2.      What sections did you find to be useful

3.      What sections do you feel could use improvement, and in what way

4.      What new sections would you like to see in the next edition

5.      Comments concerning the videotapes are also encouraged.

Please email Hazel (sive@wi.mit.edu) Rob (rmg9p@virginia.edu) or Richard (harland@socrates.berkeley.edu) with your comments and suggestions

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