D1214 Nucleic Acids Research, 2012, Vol. 40, Database issue Figure 3. Resolution of contamination groups. A contamination group contains predicted insertions in different lines that share very similar insertion positions (within 50 bp at most). After the conﬁrmation process, only one line is conﬁrmed, the others failed and are con- sidered as contaminations. When searching for insertion alleles in SimpleSearch, the user is guided to conﬁrmed allele if the contamin- ation group is solved. and leads the user to the conﬁrmed allele within a (resolved) contamination group (Figure 3). Until September 2011 about 1250 possible contamination groups could be solved and the information is available in SimpleSearch. As a result of various actions addressing data quality, including those mentioned above, the quality of the col- lection has been improved signiﬁcantly. This is best quantiﬁed with the increase of the conﬁrmation rate from 78% to 84%. Without information from the unique in-house conﬁrmation process that is carried out at GABI-Kat, this big step towards improved reliabilty would have been impossible. With a total of 21 005 genes that are covered with in- sertions [counted are ‘gene hits’ if no UTR is annotated, ‘promoter hits’ and ‘TS2TE hits’ (which include ‘CDSi hits’)], the current database release v24 covers about 4000 more genes with (predicted) insertion alleles than described earlier (7). This also includes genes for non-coding RNAs (ncRNAs), which were not annotated in TIGRv5. Due to the small size of many ncRNA-coding genes, the coverage is fairly low (182 of 1290 for ncRNA genes), which also affects the statistics of total gene hit coverage. The total coverage of the nuclear protein coding genes with (predicted) insertion alleles has increased from 64% to 70%. Changes in the web interface The static part of the GABI-Kat website is realised with an Open Source CMS system. SimpleSearch is embedded into this website, and the dynamic pages were developed in PHP. Information about individual items in SimpleSearch, e.g. a given line or a list of hits in a given gene, can be accessed by a deﬁned URL format (see the help pages of the website). Both the static and the dynamic part look identical to the user. Besides visual improve- ment, the information content has been extended. When searching for insertions, SimpleSearch now offers an overview of insertion alleles and their availability. Lines already donated to NASC (blue triangle), insertions that failed in the conﬁrmation process and are therefore un- available (red triangle), and lines available for entering the conﬁrmation process at GABI-Kat (green triangle) are distinguished. In case that a line with a failed conﬁrmation attempt belongs into a solved contamination group, the correctly conﬁrmed line for the insertion is linked in the SimpleSearch interface, which enables the user to access the conﬁrmed line easily. In addition to the existing options to search for single lines, FSTs, hits in a given gene or by BLAST, we added a search option that lists all (predicted) insertion positions in a position range on the pseudochromosomes. Perspective The GABI-Kat resource has served the A. thaliana com- munity as a valuable tool for reverse genetics since it was made available to the public in 2002. The demand for GABI-Kat insertions was constantly high since then, which is documented by the number of about 72 000 stock requests at NASC until February 2011. Until September 2011 9644 different conﬁrmed GABI-Kat lines have been donated to the stock centre. In addition to continue to conﬁrm and deliver insertion alleles to users, we are currently addressing about 760 lines with new insertion predictions in genes for which no allele is available in the other main FST-based A. thaliana Col-0 insertion line collections. SimpleSearch offers an easy and well-featured access to data about GABI-Kat lines and conﬁrmed or unconﬁrmed insertion alleles. To maintain the quality, it is important to constantly curate the database and adopt it to the most recent knowledge about the A. thaliana genome, e.g. an upcoming v11 A. thaliana genome release. In parallel, we are also working on additional topics, which could be improved. One problem arises from (short) FSTs that are assigned to genes of which paralogous copies exist in the genome. In such cases the insertion position prediction and the assignment to a single locus is error-prone. It is a challenge to represent the ‘paralog problem’ in the database, and to address it experimentally quite some wet-lab work would be required. This example shows that there is still room for further improvement.