2016-09-16 Some new FST accession numbers obtained from ENA included in SimpleSearch
About 6 weeks ago we submitted some additional FSTs to ENA for getting accession numbers. These have now been provided by ENA and were incorporated into SimpleSearch. An example is the FST 23-K121193-0022-588-G12C-8409 (line 588G12, AccNo LT615065, indicating a hit in At3g47770) which has been obtained by chance while attempting to confirm the insertion prediction in At3g47750.
2016-08-30 New database release and expert download flat files based on Araport11
Between 2016-08-15 and 2016-08-29 we have made a new database version available, and also new versions od the flat files with the database content. The db version number is "GK release 28" (see here) and includes data from 77,034 lines with genome hits. There are 23,582 genes with hits, and there are 14,235 CDSi regions (of protein-coding genes excluding pseudogenes) with hits. The sequence is still from TAIR9, but the annotation is Araport11 (which is also based on the TAIR9 genome sequence of A. thaliana Col-0).
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.