2015-08-20 Final report for GKat (GABI-Kat) submitted to PtJ
Since funding of GABI-Kat did terminate on 2014-12-31, we had to prepare and submit the "Final Report" for the GKat project to PtJ (Projekttraeger Juelich). We were a bit late and got "reminded" by PtJ. In the context of preparing the report, the "output statistics" have been updated with new numbers. As of the end of 2014, about 255,000 stocks have been distributed to the Arabidopsis community via NASC and ABRC (see here). About 56 percent of the CDSi alleles predicted within the GABI-Kat collection have been donated to NASC (see here). This means that there are about 6,000 CDSi alleles (alleles that have a very good chance to be NULL, so a real knock-out) in the population that are not yet confirmed and secured. Since the germination rate of the seed that we have in stock is decreasing, the prospects for this material are not very good.
2015-05-29 CMS tool for GABI-Kat website updated
The "engine" of the GABI-Kat website has been updated. Joomla! is the content management system (CMS) we use to maintain this site. Note that only the "static" part of the website is provided via Joomla. The dynamic parts like the SimpleSearch tool are generated by using PHP.
2015-05-17 Keeping the GABI-Kat service alive
Funding of GABI-Kat did terminate on 2014-12-31. We thank PtJ/BMBF (German Ministry of Education and Research and the Projekttraeger Juelich) for many years of very helpful funding. We, that is some people from the "Plant Genome Research" group at Bielefeld University (Weisshaar lab), try to keep the community service alive. However, due to lack of hands and time, we might be slower than before. The "GABI-Kat Team" is now a very small team that usually needs to do quite some other jobs. It took until today (Sunday, 2015-05-17) to update the homepage, to update the GABI-Kat history page, and to write this note.
2015-05-06 Delivery of seed in 2015
During the last weeks, we were able to get some of the new seed requests in queue confirmed. We are now referring to our project as "GABI-Kat III". Quite some seeds left our lab today.
2014-11-03 SimpleSearch now includes not-yet-submitted FSTs
From time to time it happens that we detect insertions that have not been predicted on the basis of a FST. Most of these cases happen when we do get a "confirmation amplicon", but the sequence of this amplicon does not fit the predicted insertion site. We use these "wrong sequence results" to deduce a new insertion site prediction, and these "ConfSeq predictions" enter the confirmation process resulting often in a positive result for the new predictions. We generate FST equivalents from the sequences we got, and these are also submitted to ENA/GenBank. However, to avoid the need for submission of very small batches of sequences, we allow SimpleSearch (since September 2014) to display FSTs that are "queueing for submission to ENA/GenBank". An example is line 038B07.
2014-10-18 Paper describing the primer design tool published
The tool for design of primers which we implemented in the context of SimpleSearch - see GK primer tool - has been published in Plant Methods (Kleinboelting et al. (2014)). As of today, the paper is also available via PubMed. In case you run into trouble with the tool, please contact us at infogabi-kat.de. Obviously, we would also be happy about positive feedback.
2014-07-24 Update of the new primer design tool
Recently, a new tool for design of primers has been made available in the context of SimpleSearch - see GK primer tool. The tool allows designing primer pairs ("amplimers") for any position on the A. thaliana pseudochromosomes. It aims at designing primers that have as few as possible misannealing sites in the genome, and it is capable of working in paralogous regions of the genome. Now, we have improved the output format to allow easy access to information about potential "confirmation amplimers" and also the amplicon that should only be build from the wt allele. Note that the automatically generated suggestions for "your insertion allele of interest" need manual checking! The automatic procedure must rely on ideal insertions that are commonly defined from LB to RB (with cut positions in the two border sequences according to textbook knowledge), but in reality the individual insertion in a given allele can differ a lot from the "idealised standard case".
In addition, some minor bugs have been fixed.
2014-05-13 DB version GK-27 released
We released another version of the content of our database (GK release 27). In the new release we have taken into account the possibility of multiple correct insertion site predictions from single FSTs. This may happen if a line contains more than one T-DNA insertion (insertions at different loci in the genome), which is the rule and not the exception in A. thaliana T-DNA lines. Due to the method used for the FST generation, different parts of the FST sequence might be derived from different loci. In such cases, fragments of different lengths for the different loci are sequenced in one sample. The shorter fragment might be represented in the front (5') part of the FST sequence and the longer fragment in the later (3') part. A new evaluation of the FSTs, which allows more that one prediction from a single FST, is represented in the new DB release and lead to an increased number of promising insertion site predictions. The new insertions can be ordered via SimpleSearch. Further information about the current DB version are listed on the DB version info page.