2016-08-20 Database content and content statistics updated to Araport11
The information displayed on the GABI-Kat database content statistics page has been updated to Araport11 values. At the same time, the database content regarding insertion site annotations is now also based on Arabort11. GABI-Kat insertions located in genes newly included in Araport11 can be identified, as well insertions that are present in UTRs which are more exactly described in the new A. thaliana genome sequence annotation.
2016-08-19 Menue of the website updated to allow more direct access to SimpleSearch
The menue of the GABI-Kat website has been changed to allow more direct access to SimpleSearch. The "link collection" that was shown until yesterday before the search interface was available has been moved to the "SimpleSearch help" page. The information about the GABI-Kat database content statistics has been moved to a new page.
2016-07-20 Step-by-step update of the GABI-Kat database to Araport11
We have started to migrate the GABI-Kat database as well as SimpleSearch to the new Araport11 Arabidopsis thaliana genome annotation dataset. The first signs are links to Araport11 on the "Line and FST details" (see this example of the 007C10/At3g27810 insertion allele) pages of SimpleSearch. Links to [TAIR], [MIPS] and [SIGnAL] are still also provided.
2016-04-30 CMS system for the static part of the GK website updated
We have updated the Joomla system that we use to manage the GABI-Kat website to Joomla v3.5.1. The Joomla version used before was v2.5.28. If you recognise "funny" design problems please perform a "shift-reload" of our page or purge the cache of your browser. We had to update the style sheets which are kept in cache. The PHP part of the website that presents the dynamic pages with data from the GK database is unchanged.
2016-04-10 Problems due to illness of co-workers partially overcome
Since the end of December 2015 we had serious trouble due to illness of the remaining co-worker in the lab. This resulted in almost complete outage of wetlab work. Now, the problem has been at least partially solved since we were able to re-activate a former co-worker. Last week, the first seed for 2016 did leave our lab. Our hope is that the accumulated backlog will be resolved in the coming weeks.
2016-01-09 FSTs from TDNA-Seq analysis of GABI-Kat lines done at SALK incorporated
About 10,000 GK-lines that were selected for TDNA-Seq have been analysed at SALK (O'Malley et al., in preparation). You can find the "hits" in SimpleSearch.
2015-11-14 More than 13.600 lines donated to NASC
Batch number 151 containing 100 newly confirmed GABI-Kat lines has just been donated to NASC. This is the first batch donated after public funding of GABI-Kat ended at 2014-12-31. We are on the way to reach 14.000 GK lines at NASC; we expect to donate about 275 additional lines by the end of 2015. See here for exact numbers of donated lines.
2015-11-02 Paper about analyses of insertion sites published
By using the confirmation sequence data that accumulated at GABI-Kat, and also by systematically addressing the 2nd border of about 1,200 insertions that had been confirmed at one border, we generated a large dataset describing the structure of T-DNA insertion sites. These data are now available in print and appeared in MOLECULAR PLANT 8:1651-1664 (2015). The title is "The structural features of thousands of T-DNA insertion sites are consistent with a double-strand break repair based insertion mechanism." by Nils Kleinboelting et al.. Also, Nils defended his PhD thesis which included data from this paper in July 2015.