Several months ago, we have started to prepare for stopping the GABI-Kat confirmation service at some time in the future. This service is running since more than 15 years. The reason is that the number of requests is declining (although there are still quite some requests for GABI-Kat insertion lines). In addition, the administrative overhead for handling the requests is getting crazy.

To allow the Arabidopsis community access to “valuable” GABI-Kat insertion alleles even if the line has not yet been confirmed and donated as T3-set to NASC, we will start donating T2-stocks. Obviously, these lines/insertion alleles are NOT confirmed but are donated on the basis of predictions. However, the in-house confirmation rate at GABI-Kat is about 80% which indicates that there is a good chance to confirm the predicted insertion allele after ordering a T2-stock from NASC. Lines that have been donated to NASC as T2-stocks can not be requested from GABI-Kat. Information about which lines have been donated is available from SimpleSearch. An example is here.

A paper describing new features incorporated into SimpleSearch and the GABI-Kat database has just been published in PCP (see here). The most relevant point was the switch to the Araport11 annotation. 

Batch number 157 containing 99 newly confirmed GABI-Kat lines has just been donated to NASC. We are on the way to reach 15.000 GK lines at NASC; we expect to donate about 75 additional lines by the end of 2016. See here for exact numbers of donated lines.

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. 

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).

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.

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. 

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.