BrassicaDB hits 3 GB! BrassicaDB has just been rebuilt from EMBL release 75.

BrassicaDB has been rebuilt from EMBL release 74. Nearly 600,000 B. oleracea GSS sequences have been mapped in silico against th\ e Arabidopsis genome. Absolute chromosome coordinates of homologues, together with names and descriptions of corresponding gene models are now stored in Bra\ ssicaDB and are fully searchable.

AGR has been rebuilt with 57,725 new Insert_salk.

BrassicaDB has been rebuilt from EMBL release 72 and now contains more than 420,000 DNA sequences, most of which are from the TIGR/CSHL B. oleracea shotgun sequencing initiative.

A single chromosome of the grass Festuca pratensis has been introgressed into Lolium perenne to produce a diploid monosomic substitution line. The substituted F. pratensis chromosome has been mapped with 104 EcoRI/Tru91 and HindIII/Tru91 AFLP markers, generating a map of 81cM which is now available in FoggDB.
An updated version of "S and Z genotyping and mapping in ryegrass" has been released, including more information about progeny alleles and S locus distortion on linkage group 3 of Lolium perenne.

Please note that the ARS Genome Database Resource (GDR) server formerly at http://genome.cornell.edu and http://ars-genome.cornell.edu is now permanently off-line. We are continuing to mirror databases previously associated with this site.

25/07/02 - BrassicaDB

BrassicaDB has been rebuilt from EMBL release 71. We have discovered there are software issues with the new server that have broken the PCM and Recombinant Viewer displays for genetic map data. We will fix these as soon as possible.

28/06/02 - BrassicaDB

The rebuild of BrassicaDB from EMBL release 70, including some 300,000 B. oleracea GSS sequences, is now available on this site. Please report any problems to the BrassicaDB developer. Meanwhile, the rebuild from EMBL r71 is already in progress!

8/02/2002 - BrassicaDB

This has been the most complex rebuild of BrassicaDB yet, thanks to the 200,000 or so Brassica GSS sequences recently published by a joint initiative between CSHL and TIGR. We are currently running a massive BLAST analysis on these sequences and will add the data over the coming weeks. We are also moving to new server and client software, which is still being tested. Click here for a preview of the new BrassicaDB, coming here soon!

November 2001

1/11/2001 - New genetic map in FoggDB

The Forage Grass Genome Database FoggDB now contains a new genetic map of Lolium perenne produced by members of the International Lolium Genome Initiative (ILGI), with data contributed by labs in Australia, the UK, Japan and France. There are 240 loci covering 811 cM on the 7 linkage groups, and the markers used include 109 barley, rice, oat and wheat anchor probes.

October 2001

11/10/2001 - FTP site directory changed
The FTP site has changed directory structure. All the files are now tar'd and gzipped up.

June 2001

22/06/2001 - Brassica IGF project
A sister database to BrassicaDB has been set up to contain BAC physical mapping data, integrated with the Arabidopsis genome through clone hybridisation. It now contains the first wave of contig assembly and hybridisation data. Check the project website for details.

April 2001

27/04/2001 - New BrassicaDB maps
BrassicaDB now contains genetic maps for Brassica rapa developed in a collaboration between BBSRC and AAFC's Saskatoon Research Centre.

March 2001

14/03/2001 - New UK BLAST database
To expand the range of BLAST databases on our UK CropNet BLAST server we have added the option of BLAST searching against just Arabidopsis ESTs (over 110,000 sequences).

14/03/2001 - New UK CropNet database
UK CropNet are please to announce the launch of a new database - CropSeqDB. This database serves two main purposes. Firstly it acts as a repository of sequences from UK crop species (nearly half a million sequences from over 100 species). Secondly, these sequences have been linked to our AGR database through exhaustive BLAST analysis. So if you have a gene of interest in a species such as Barley, then you can find it in CropSeqDB (search by EMBL accession, gene name, or gene product) and see what the most likely homologues in Arabidopsis will be. CropSeqDB can also be searched by using our UK CropNet BLAST server facility.

08/03/2001 - New markers in BrassicaDB
BrassicaDB now contains some 400 BBSRC-funded microsatellite markers and maps using these SSR markers are now being developed.

February 2001

08/02/2001 - New database
We now have kindly been given permission to mirror the CompositDB database from the group at UC Davis. Many thanks for letting us add this database to our collection!

January 2001

12/01/2001 - Improved BLAST server
The UK CropNet BLAST server now allows you to search against all five completed Arabidopsis chromosomes. Very useful for when you want to know where exactly your gene of interest lies. The complete chromosome sequences are available at the MIPS FTP site.

November 2000

27/11/2000 - New InsertWatch facility
NASC have launched a new facility which builds on the insert blast server which was launched a few months ago. The new facility is called InsertWatch and lets you submit genes of interest (or any sequence) to a private database held by NASC. Following submission, users are immediately told whether there are any Arabidopsis insert sequences that match their sequence. Additionally, NASC will then search any new insert sequences that we receive against the submitted sequence and email the user if and when there are any new matches. That email will contain details of the blast alignment along with links to the NASC stock catalogue to allow users to order the corresponding insert lines.

10/11/2000 - New search page for AGR
Because AGR contains so much information, it can be a little bewildering when trying to search the database. Our new AGR search page tries to make things a little easier and offers helpful tips.

10/11/2000 - Presentations page
Download some Powerpoint presentations of talks given by UK CropNet members.

September 2000

25/09/2000 - Everything improved!
UK CropNet is now running off a new server which is many times faster and more powerful than the old server. This means we can store many more databases and try out new facilities, such as the option to perform a BLAST search against any of our (sequence containing) databases. Most importantly, with 2 Gb of memory everything should now seem a lot faster when accessing/querying any of our databases (particularly when a lot of people are connected at once)!

We've also taken the time to improve the look of the AceBrowser interface to our databases, e.g. try searching for an author. It should now be easier to find the information that you want. Oh, and we've also added a Google search facility to every page so that you can search either the entire web, or just UK CropNet. We hope you like the improvements!

August 2000

15/08/2000 - New Arabidopsis EST information available
Many thousands of new Arabidopsis ESTs have recently become available. These sequences are derrived from many different plant tissues. To access over 100,000 Arabidopsis ESTs and to find out more about what plant tissues these ESTs come from, click here.

July 2000

14/07/2000 - Details about UK CropNet training sessions
There is now a page which highlights the forthcoming dissemination sessions that are regularly held by UK CropNet. These training events are open to anybody who wants to know more about what we do, and who wants to know more about how to use our databases.

07/07/2000 - Web site award

The UK CropNet website has been designated a 'key resource' in the topic of Plant Genome Databases by Links2Go.

06/07/2000 - Improved version of AGR released
The AGR database has now been rebuilt to allow for faster access and to cope with the additional information that it now contains. Two new classes of information have been added to allow you to search gene name and gene product descriptions. Extra information has also been added with regard to insert sequence descriptions (see the AGR insert page for more details) and it is now easier to focus searches on just the clones and sequences involved in the Arabidopsis Genome Initiative (AGI).

May 2000

23/05/2000 - Improved insert information and BLAST server
In response to the growing interest in insert sequences for Arabidopsis (i.e. "is there a line of Arabidopsis available which has my favourite gene disrupted by an insertion?"), we have created a special AGR insert page to allow you to find out more about the insert sequences that are stored in our AGR database. Supplementing this page is an insert BLAST page on the NASC server. This page allows you to search your sequence against all available insert sequences in AGR.

18/05/2000 - IMA insert information now in AGR
Information from the published table of Ds insertion sites ( Plant Cell, 1999, 11, 2263-2270) has been integrated into AGR. You can now ask AGR to list all sequences which contain a putative insertion site (either SINS or IMA). See the AGR insert page for more details.

April 2000

17/04/2000 - Trial BLAST server
We are currently experimenting with a web-based BLAST server which contains all AGR, BrassicaDB, FoggDB, and MilletGenes sequences (nucleotide and protein). Click here to access this service.

17/04/2000 - BrassicaDB expanded
BrassicaDB now contains B. napus, B. oleracea and B.rapa nucleotide and protein sequences.

17/04/2000 - Web site award
The UK CropNet website has been voted web pick of the day by HMS Beagle

10/04/2000 - New look AGR page
The Arabidopsis Genome Resource (AGR) page has been updated and now offers many new starting points for retrieving information from the AGR database. It is now (hopefully) easier to find information in AGR.

March 2000

20/03/2000 - New database mirrored
Cropnet now mirrors the Alfagenes database from Cornell University. See the database page for more details.

20/03/2000 - New look to website!
Hopefully it should now be much easier to navigate the CropNet site. There is now more information and more help (particularly with respect to accessing our databases).

February 2000
2/2/2000 - Approximately 15,000 new sequences have been added to the Arabidopsis Genome Resource (AGR). These sequences are all genome survey sequences (GSS) from the Landsberg erecta ecotype and have been released by The Institute for Genomic Research (TIGR).

January 2000
The following article about the databases and software available from UK CropNet was published in the January 2000 issue of Nucleic Acids Research and is available by selecting from the relevant link below: