XINE v2 issue 1
Dear colleagues,
Welcome to XINE, a Xenopus newsletter intended to disseminate information to the field at large. Currently, the newsletter is distributed whenever there is news to report. A monthly or bi-weekly format would be preferable but this depends on contributions of information from Xenopus investigators (not much coming in so far). If you have anything that you would like the community to be aware of, please e-mail the editor, Bruce Blumberg (blumberg@uci.edu) who will include it in the next newsletter.
Important new resources for Xenopus genomics!
There are several important resources coming online for Xenopus ESTs and genomics that are of considerable interest to Xenopus researchers. These resources are the focus of this issue of XINE
Xenopus climbing up the EST list
Here are the current counts for the top 10 EST organisms as of Feb 15, 2002. As you can see, Xenopus laevis has now passed zebrafish and is closing fast on Drosophila, bovine and soybeans.
| Homo sapiens (human) | 3,967,060 |
| Mus musculus + domesticus (mouse) | 2,519,654 |
| Rattus sp. (rat) | 326,707 |
| Drosophila melanogaster (fruit fly) | 255,456 |
| Bos taurus (cattle) | 230,256 |
| Glycine max (soybean) | 225,709 |
| Xenopus laevis (African clawed frog) | 197,588 |
| Caenorhabditis elegans (nematode) | 191,268 |
| Danio rerio (zebrafish) | 187,310 |
| Lycopersicon esculentum (tomato) | 146,825 |
Xenopus tropicalis is in 26th place with 43,464 ESTs and gaining fast. Thanks to everyone involved in making these resources available.
Xenopus laevis EST resource now available to the public
Professor Naoto Ueno and his colleagues at the National Institute for Basic Biology, Okazaki, Japan have developed a collection of more than 70,000 ESTs from three stages of Xenopus laevis. Professor Ueno has now opened this resource to the public where it may be accessed at http://xenopus.nibb.ac.jp/
Professor Ueno provides these notes for users of XDB
1. Keyword search is available only for "contigs". We are now trying to
prepare for searching in "singlets",too.
2. Singlet page is now under construction. But BLAST hit list table and sequence itself
are already able to be browsed.
3. We are now updating with the versions of NCBI Xenopus Unigene (Build #9), and TIGR XGI
(release 2.0) for BLAST search.
4. We will send the clones upon users request.
Xenopus laevis EST database presented by NIBB
XDB
Opened to public on February 25 (MON) at
http://xenopus.nibb.ac.jp
Useful features include…
A large number of ESTs (more than 7x104) from three different embryonic stages.
Powerful search system based on clone name and contig name in addition to conventional BLAST and Keyword search.
Seamless link to Xenopus Unigene (NCBI), Xenopus Gene Index (TIGR) and Genome Net Japan (Kyoto Univ.)
NCBI Xenopus protein DB data are added to Xenopus BLAST hits.
In the future…
Comprehensive expression profile data by in situ hybridisation and DNA array will be integrated.
Linked to Axeldb and other Xenopus genomics-related databases by an exchange server.
Xenopus tropicalis EST project now online
The Wellcome Trust Sanger Institute in collaboration with the Wellcome CRC Institute in Cambridge has initiated an EST project for Xenopus tropicalis. Details may be found here http://www.sanger.ac.uk/Projects/X_tropicalis/
The Sanger Institute expects to generate up to 50,000 5' EST sequences from each X.tropicalis cDNA library supplied. These sequences will be analyzed and stored in an Acedb database, TropAce and can be searched using the blast server or downloaded from their ftp site.
Queries concerning this project can be sent to trop@sanger.ac.uk.
Washington University of St. Louis EST project
WashU has generated the majority (114,994) of Xenopus laevis ESTS in the current database. You can access their Xenopus EST site here http://genome.wustl.edu/est/xenopus_esthmpg.html.
Xenopus UniGene sets
Xenopus laevis is now a UniGene organism (one of only six). Practically speaking, this means that the data generated from EST sequencing are being clustered and compared to identify groups of ESTs derived from the same gene. Using the UniGene database, one can readily determine whether an EST of interest is unique or if there are other ESTs from the same or other libraries that overlap. This will enable the rapid detection of full-length ESTs. For more details, visit the Xenopus UniGene site at http://www.ncbi.nlm.nih.gov/UniGene/Xl.Home.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