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.
2013-04-24 New features in the publication list
The publication list on our website has been updated with new features. In case that we have detected specific GABI-Kat alleles that were used for listed publications, the respective lines are linked directly from the paper entry. The allele names chosen in the publications are indicated in the links. If no allele name was chosen, the GABI-Kat line ID is indicated.
This feature is not comprehensive but it will be updated when we find new publication-to-line/allele links.
2012-12-19 Delivery of more seed delayed to January 2013
During the last weeks, the last seeds of newly confirmed lines have left the lab for 2012. Since the coming holidays may interfere with international delivery, the next seed will be put into the mail not before the second week of 2013.
We wish all our users a Merry Christmas and a Happy New Year, and GREAT phenotypes for the experiments in 2013!
2012-12-03 Visualisation tool updated to a fully new version
We have updated the tool in SimpleSearch that visualises the insertion positions of (predicted) T-DNA insertions in the A. thaliana genome. The new tool has been newly written from scratch, with contributions from Nils Kleinboelting and a number of students from the BSc and MSc curricula "Bioinformatics and Genome Research" of Bielefeld University, including Benedikt Brink and Andreas Kloetgen. The new tool has the following main features:
- Confirmation sequences are displaid graphically as "mapped" bars. This tells the location of the insertion as deduced from the confirmation data.
- For an increasing number (but not yet all) of confirmed insertions, the predicted AND the updated insertion position is shown.
- It is now possible to switch between a "Insertion view" and a "Line view". The line view shows the data for a single line including (if available) the confirmation sequences and primers, while the insertion view shows all insertion predictions mapped to a given genome region.
- In the insertion view, higher numbers of insertion predictions that are placed to a single locus are collected in a "multi triangle". Multi triangles (see the larger triangles here) may resolve into individual triangles when you zoom in, and vice versa.
An example is available here for insertion view, and here for line view.
2012-12-02 SimpleSearch update went public
The SimpleSearch interface has been updated to allow better access to genotyping and primer information. There is now a page that displays the data for each insertion allele for that we had success in the confirmation process. This additional function is mainly relevant for DUPLO, but it is also helpful for "normal" GABI-Kat alleles. An example for a "normal" GK allele is this one: 220B01/At2g40950; and an example for a GK allele that contributed to DUPLO is 144H10/At5g42000. Also, quite some small bugs and glitches have been fixed.
In addition, a bug in the "Search for genome range" search code was fixed that prevented the display of intergenic insertion predictions. Now, the insertions listed for a genome range should be all available insertion predictions, sorted according to the prediction insertion position. Example for a region on chromosome 4.