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XINE volume 4 issue 2

Xine Volume 4 issue 2 - February 2004

Dear Colleagues:

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


Xenopus tropicalis genome project

X. tropicalis genome assembly 1.0 is the first of a series of preliminary assembly releases that are planned as part of the ongoing X. tropicalis genome project. It is a very early step towards the complete draft genome of X. tropicalis, and is based on only the first ~2.2X depth of sequence coverage in end-sequence from small insert plasmids that was available in November 2003. Sequence is accumulating and users should expect steady improvements in the quality and length of assembled contigs and scaffolds in future releases. The next preliminary assembly is expected to be released by the end April, 2004 and include approximately 4X 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. Preliminary assemblies like version 1.0 are an attempt to provide value to users throughout the life of a sequencing project, beyond the redundant and highly fragmented raw shotgun data. Like any preliminary scientific result, it is incomplete and may contain errors that may be expected to be corrected and refined as the project progresses. Note that, as described in more detail below, the limited sequence data at 2.2X permits only relatively short (few kilobase) regions of contiguous sequence to be recovered, and these "contigs" can only be linked into short (tens of kilobase) scaffolds. (A "scaffold" is a reconstructed genomic sequence that may contain one or more gaps (marked by runs of "N") whose size can be roughly estimated.) So assembly 1.0 is necessarily quite rough.

We ask users of this data who require complete genes and/or high quality sequences to recognize the limitations in the current assembly and to be patient. We are working as quickly as possible to accumulate sequence and provide timely assemblies. In the meantime, we hope that even with these caveats,) these early glimpses of the X. tropicalis genome provide a useful resource to the scientific community. Please stay tuned. 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 (http://www.genome.gov/page.cfm?pageID=10506376) 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). More detailed information about the project plan and methodology will be posted on the JGI web site (http://www.jgi.doe.gov/xenopus) shortly.

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


Xenopus microarrays

Following is a request from Ken Cho concerning X. laevis microarrays. Ken is establishing a center to produce chips for the Xenopus community and has a grant pending. The following information would enable him to answer criticisms of the reviewers and get the center up and running.

Dear colleagues,

I plan to resubmit a Xenopus microarray center grant proposal and need to address the following specific criticisms. The grant reviewers would like to know the usage patterns of the Xenopus chips.

1) If we can supply ~15,000-20,000 unigene set microarray chips at the price of ~$100/slide, are you interested in using them?

2) If we provide fee-for-service assistance to do hybridization and preliminary analysis, are you interested in using the service?

3) How many chips do you think you will use in one year (include both laevis and tropicalis)? Do not forget that each array experiment must be repeated several times (It is better to overestimate than underestimate).

Please respond via email to kwcho@uci.edu


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
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http://blumberg.bio.uci.edu/xine/index.htm
http://www.xenbase.org/xine/xine.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

 

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