2014-04-07 Database content now fully based on TAIRv10
Since quite some time we worked on updating all datasets in SimpleSearch to transfer them to TAIRv10. Although this was already done for FSTs and new wet-lab data in 2011, the update of older confirmation data was not complete because manual interaction with the data to be updated was often required. Now we completed the update of all confirmation data that were generated in GABI-Kat since 2001. Our recent efforts allow a more precise determination of the exact insertion sites in our lines based upon the confirmation sequences (instead based upon FSTs only) as well as a complete representation of the data in our visualisation tool.
2014-03-27 Primer design tool in SimpleSearch available
A new tool for design of primers has been implemented into SimpleSearch. It allows to design primers at any nucleotide position on A. thaliana pseudochromosomes. The primer selection procedures used by the tool are those used at GABI-Kat for designing gene-specific confirmation primers. These procedures have been optimised over years to contribute to improved confirmation rates. The tool can be accessed through the SimpleSearch menu entry GK Primertool and is currently in the beta state. Minor adjustments may be implemented in the next days. The tool aims to design primers that have as few as possible misannealing sites in the genome, and it is capable of working in paralogous regions of the genome.
2014-03-26 Extension of the GABI-Kat grant to December 2014
The presently running GABI-Kat grant from PtJ/BMBF (German Ministry of Education and Research) has been extended until 2014-12-31. We may be able to submit an extension proposal to continue the service to the community, but it seems that the chances for a positive decision about such a proposal are low.
2014-03-20 Gene search function in SimpleSearch improved
We adjusted the gene search function in SimpleSearch. After confirmation of requested insertions, the FST-based insertion position is corrected according to the confirmation sequences in our database. Due to this correction the affected gene might change. In our visualisation tool this is illustrated by dark blue and light blue triangles. You might want to check the example 011F01, where the gene code has changed from At5g05170 to At5g05180. The gene search function was able to find the FST-based prediction, only. Now it is also possible to find the corrected and more accurate position, when the gene code of the insertion position has changed.
2013-08-13 Improved reliability of FSTs in SimpleSearch
The analysis of groups of FSTs in the SimpleSearch db has shown that in rare cases the insertion site predictions in selected lines was incorrect. In such cases we removed the respective FSTs from SimpleSearch. Consequentially the data integrity in SimpleSearch could be improved through this procedure. Yet, it is possible that using the search form delivers different/less results than before. Such differences should be very rare, though. You might want to check the help page for more information on possible error messages.
2013-07-22 GABI-Kat affected by the global financial crisis
The bank account at WestLB, which has been used for the reimbursement for the delivery of GABI-Kat seeds should not be used anymore. We ask our users to use the new bank account at the Landesbank Hessen-Thüringen, instead. Details can be found in the Download area. The document "Notes of ordering lines and supplier info" has been updated.
2013-06-25 Google-Scholar profile of GABI-Kat available
We implemented a Google-Scholar profile of GABI-Kat. In this profile the most frequently cited publications of GABI-Kat are outlined. These publications are linked to the citing papers within Google-Scholar.
2013-06-01 Suddenly appearing problem with visualisation fixed
Between 20130530 ans 20130601, a problem appeared that caused malfunction of the insertion allele visualisation tool. The tool failed to show the insertion location, it only displaid the error message: "Fehler beim Zeichnen der Grafik!" (this is German and means: "Error when drawing the diagram"). The problem was fixed on 20130601 (thanks to Torsten). However, at present we are not sure if it will show up again, we are searching for a permanent solution.