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.
2014-04-10 DB version GK-26 released
With the recent submission of additional FSTs we released an update of our database (GK release 26). The details about the current DB version are listed on the DB version info page.
2014-04-08 SimpleSearch data content extended
About 1500 new FSTs have been submitted to EBI/ENA and GenBank (HG967694 to HG969186), and the corresponding data are also available from SimpleSearch (see DB version info for details). In addition to these FSTs, which are for GABI-Kat lines, we have submitted 40 FSTs for SALK lines (HG967654 to HG967693). The SALK FSTs were produced in the context of the former project GABI-DUPLO. Further information on SALK lines, which were confirmed for the GABI-DUPLO project is available here.
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.