Xenbase: a Xenopus web resource

Xine Volume 4 Issue 4 - September 2004

Dear Colleagues:

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

Xenopus laevis genome sequencing update

You may remember that Don Brown was spearheading a proposal to JGI's Community Sequencing Program that requested sequencing of the Xenopus laevis genome as a complement to the ongoing effort to sequence the X. tropicalis genome. Don reports that this effort was not successful and, furthermore, that JGI will not be sequencing any proposals for more than 1 Gb of sequence in the coming cycle. This precludes any genome-wide sequencing of X. laevis. You can view the review of the proposal at http://blumberg-lab.bio.uci.edu/xine/brown.pdf

If there is someone in the community who wishes to take up this effort and perhaps submit a proposal to NIH or NSF, Don would be very happy to contribute the proposal that he and his group worked on as a starting point.

From the Sanger X. tropicalis EST team

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/

Release notes follow. Files should become available over the next 24hrs as the external ftp site is updated.

I am very pleased to say we are now through the 300k accepted ESTs
barrier!

Best regards (on behalf of the Sanger team)

Mike Croning, D.Phil.
Informatics Team, Sanger Institute
01223 834244 x7282
www.sanger.ac.uk/Users/mdr/cv/

X.tropicalis FTP site notes

Release date: 16/07/04

Here follows a summary of the X. tropicalis EST sequences available from the Sanger FTP site, and public databanks, produced as part of the Sanger Xenopus tropicalis EST project 2001-2004, sequenced from the Xenopus Gene Collection (XGC) libraries constructed by Aaron M. Zorn and Nigel Garrett.

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

EST LIBRARIES

Tneu neurula stage embryo library 63604 seqs
Tgas gastrula stage embryo library 62323 seqs
Tegg egg library 64367 seqs
TtpA tadpole library 42860 seqs
TtbA tailbud library (stage 28-30) 42523 seqs
ThdA tailbud head (stage 28-30) 29927 seqs

Total EST sequences: 305604 accepted sequence

From Steve Klein:

There's a new Program Announcement from NIGMS that should be very useful for the Xenopus Community. It's called "TOOLS FOR GENETIC AND GENOMIC STUDIES IN EMERGING MODEL ORGANISMS". You can get the whole PA at http://grants2.nih.gov/grants/guide/pa-files/PA-04-135.htmlThe major goal of the PA is to support research to enhance the usefulness of sequence information for newly emerging or developing model organisms for
which there are limited genomic resources. Objectives to be addressed in applications submitted for this PA include, but are not limited to, the
following:

• Improvements in tools for mining of data for genomes having unique composition or structure,
  
• Improved database management and integration with other databases (Requests for the maintenance of databases alone are not encouraged.),
  
• Generation of comprehensive cDNA libraries,
  
• Development of microarray reagents and/or services,
  
• Improved methods for linking expression arrays with standard phenotypes or with specific biological or behavioral outcomes,
  
• Development of novel approaches for mutagenesis and for rapid identification and characterization of point mutations,
  
• Development of novel transposable element-based techniques for the generation of knockouts or other mutations,
  
• Improvements in gene transfer technology and in vectors for genomic manipulation,
  
• Generation of sets of gene knockouts or knock-downs.

Xenopus meeting update:

The 10th International Xenopus meeting is fast approaching. The conference will have a record number of participants - 350. I look forward to seeing you there and hearing your suggestions for how to approve Xine.

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

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Until next time.
Bruce