Due to Easter vacations, and because of the start of the summer lecture term at Bielefeld University, answers to questions sent by Email to info[at]gabi-kat.de had been delayed recently. We will clean up the backlog by the end of this week.

The "engine" of the GABI-Kat website has been updated to Joomla version 2.5.4. Joomla! is the content management system (cms) we use to maintain this site. The separator shown in the "breadcrumbs" has been fixed to display the small graphic that is expected, and several inconsistencies in the display of links (should be in green like the link to Joomla!) or headings (should be displayed in black) have been corrected.

We have extended the Methods collection of protocols we use at GABI-Kat by adding our protocol describing what we do if we observe (very) low germination rates in lines that we need/want to bring into the next generation.

The "engine" of the GABI-Kat website has been updated from Joomla version 1.7.x to version 2.5.x. Joomla! is the content management system (cms) we use to maintain this site. Minor glitches like the change in the separator in the "breadcrumbs" will be fixed soon.

About 3500 new FSTs have been submitted to EBI/ENA and GenBank (HE664175 to HE667735), and the corresponding data are also available from SimpleSearch (see DB version info for details). There are about 800 new lines with genome hits, and the number of CDSi hits (in protein coding genes) increased by about 300. The bulk of the data is derived from our continued efforts to produce FSTs from "weak" parts of the population. 

In addition, we have re-evaluated some unusual confirmation sequences to get access to additional insertion alleles. Sometimes, we do get an "confirmation amplicon", but the sequence of this amplicon does not fit the predicted insertion site. According to our rules, the respective insertion prediction (insertion allele) is NOT confirmed. However, we have now used these "wrong sequence results" to deduce a new insertion site prediction. These "ConfSeq predictions" then enter the normal confirmation process, and in a significant number of cases these new predictions are confirmed. We generated FST equivalents from the sequences we got, and these were also submitted.

We have updated SimpleSearch in two minor aspects: (i) the search term that a user provides is highlighted on the main output page "Line and FST details". For example, you can search for the FST with GenBank accession number AL936383 (start here), and you get this string highlighted on the output page. (ii) We attempted to unify the way the AGI codes are presented to the format At1g23450, and abandoned the format AT1G23450. 

Since 2006, SimpleSearch contains the confirmation sequences which we generate for each confirmed allele. Essentially, we produce for each confirmed allele (or insertion site prediction) two sequence reads from the confirmation amplicon. One read with the gene-specific primer, the other with a T-DNA primer. In some cases, we need to use different primers and repeated attempts to produce the confirmation amplicon and its sequence. Up to yesterday, these additional sequences were also presented by SimpleSearch, although they are useless (e.g. very low phred score during base calling) or even missleading (e.g. the two reads from the "same" amplicon hit different loci). Now, these sequence reads are filtered based on a flag in our database, and only the reads that lead to the conclusion "insertion prediction confirmed" are presented. 

Several batches of newly confirmed GABI-Kat lines have recently been donated to NASC. Today, we donated 99 additional lines (that is 1.269 different seed bags). Now, we have crossed the border of 10.000 lines donated to NASC! See here for the exact number.