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Xine v3.3

Xine Volume 3 Issue 3

Dear Colleagues:

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

There is lots of news on genomic resources for Xenopus.


New Xenopus resources at NIH

A Xenopus tropicalis Unigene web site is now online.

http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Str

The NIH Xenopus Gene Collection Website is now available.

http://xgc.nci.nih.gov/


Call for Xenopus tropicalis genes to be sequenced. BAC Sequencing for the X. tropicalis Community

The JGI is now accepting requests for shotgun sequencing of selected BAC clones containing genes of biological interest. If you have identified a BAC for sequencing or would like the BAC library screened for specific sequences, click the link below.

All requests will be reviewed and prioritized by the Xenopus tropicalis Genome Project Advisory Board.

The response to this call has been underwhelming to say the least. Marv Frazier at JGI suggests that the request be called "get your gene sequenced for free". If you want to take advantage of this opportunity, go to the following link to apply.

http://genome.jgi-psf.org/xenopus0/bacs/index.html


Affimetrix chips for Xenopus may soon be available.

Here is a note explaining the process and requesting that sequences be submitted to GenBank sooner rather than later so that they may be considered for addition to the chip during the design process

Dear Xenopus Researcher,

A public consortium of researchers has been organized to oversee the design of a publicly available expression array for Xenopus. Up to 15,600 candidate laevis expressed sequences can be represented on the chip. We felt it important to contact the Xenopus community and guarantee that up-to-date, biologically important genes are included on the chip. It is our hope that most, if not all, Xenopus laevis genes that have GenBank IDs will be included.
It is not our intention to trigger a new round of de novo sequencing projects whose completion may delay the design process which might begin as early May. To this end we are encouraging investigators to submit sequences to GenBank now (see www.ncbi.nlm.nih.gov/BankIt for sequence submission instructions). In order to maximize the overall quality and performance of the array, we encourage submission of sequences that have evidence of being expressed. The desire to have publicly available sequence and the logistics of maintaining standardized annotations require submission to GenBank for association with public identifiers.

The following is a brief overview of the design process:

• An assembly of contigs (consensus sequences) will be made for each UniGene cluster. The consensus sequence is an in silico version of the longest contiguous transcript (not necessarily full length) that is used as the target sequence for the purpose of probe design. This target sequence will reside on a public database and be linked to the GenBank accession ID sequences that were used to create it.
• Various techniques will be used to verify the quality of the sequence.
• A list of consensus sequences will be selected and ranked by representatives of the Xenopus Consortium. Along with instructions for the chip design, the sequences will be used as the template for array probe(s) selection.
• Probe and probe set selection will be reviewed prior to final approval by the representatives of the Xenopus Consortium.

Once this project is initiated, additional information on this project will be posted on Xenbase in the form of an FAQ.

Sincerely,

The Xenopus Consortium

Aaron Zorn (main consortium contact, aaron.zorn@chmcc.org), Division of Developmental Biology, Children's Hospital Medical Center
Robert Grainger, Dept. of Biology, University of Virginia
Richard Harland, Dept. of Molecular & Cell Biology, UC Berkeley
Paul Mead, Dept. of Pathology, St Jude Children's Research Hospital
Igor Dawid, Laboratory Molecular Genetics, NICHD
David Klein. Laboratory of Developmental Neurobiology, NICHD
Ken Cho, Dept. of Developmental & Cell Biology, UC Irvine
Lukas Wagner, NCBI


Here is an update on the Xenopus tropicalis EST project from the Sanger Centre

The Sanger EST sequencing and analysis teams are pleased to announce the immediate availability of an updated bioinformatic analysis of the Xenopus tropicalis ESTs sequenced by the Sanger Institute as part of the Xenopus tropicalis EST Project (http://www.sanger.ac.uk/Projects/X_tropicalis/).

The principal change in this release is the addition of a global clustering of the ESTs across the three tissue libraries sequenced so far, to complement the clustering by library we have previously provided. The subsequent analysis and visualisation of the consensus EST sequences has also been improved. Full details of the changes are outlined below.

By library clustering:
http://www.sanger.ac.uk/cgi-bin/Projects/X_tropicalis/sang_est_db_search

Global clustering:
http://www.sanger.ac.uk/cgi-bin/Projects/X_tropicalis/sang_est_db_search_all

Feedback as to the the quality of the data provided, together with suggestions of improvements, and desirable features to be implemented are, as always, warmly invited.

Regards

Sanger team


FTP SITE UPDATE
---------------
Updated data will be available today (02/06/2003) on the ftp site:

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

A fasta file containing all the analysed ESTs is provided complete with: library, public accession, clone and sequencing direction details.

Files of the consensus sequences derived from both the global and by-library EST clustering are also provided, containing details of both the library and size of the cluster from which there were derived.

DATABASE AND SOFTWARE AVAILABILTY
---------------------------------

The complete analysis databases (MySQL), together with the software package that provides the Perl API to the clustering analysis, and drives the website is available free of charge with a relaxed (BSD?) licencing conditions. Requests should be made preferably to estdb@sanger.ac.uk (subscribe first, as described in the database help), or failing that, to mdr@sanger.ac.uk.

CHANGES TO X.tropicalis EST ANALYSIS
-------------------------------------

Two complementary clustering analsyses and databases are now provided of the X. tropicalis EST set. These are produced by 'global' (new) and 'by tissue library' EST clustering (as before).

Both databases now provide an example search session to facilitate new users use of the resources, by a guided exercise to find a gene of previous interest, introducing users to the many web views available. The examples are reached by clicking the 'Example Search Session' button which is now prominently displayed on the EST_DB web search pages.

The method of consensus sequence generation from gapped alignments has been improved in order to reduce potential frameshift errors in sequences.

BLAST search results are now provided for:

Swall proteins WuBLASTX
Xenopus sp. mRNA WuBLASTN (new)
TIGR Xenopus laevis gene index (XGI) WuBLASTN (new)
UniGene X. laevis WuBLASTN (new)
Ensembl human proteins WuBLASTX (new)

All results are now presented in a new graphical overview of the consensus sequence containing all the blast results, and the ESTScan predicted protein (if any). Analysis features are separated according to the strand of the consensus from which they were generated.

Web navigation of the blast alignments, and external databases has been improved. For example, one can view the alignment of an Ensembl-predicted human protein to a translated consensus sequence, within the EST_DB website, then with a single click, view the gene from which the human protein was derived, together with chromosomal location, etc, in the www.ensembl.org website. Similarly one can view the alignment of a consensus sequence against a Unigene 'representative' EST in the EST_DB website, then with a single click view the UniGene cluster information at the NCBI to which the EST belongs.

Web page titles now reflect their specific contents, facilating website navigation. Examples are 'CloneView', 'ConsensusView and 'ConsensusTextSearchView'.


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

Until next time.

Bruce

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