Published online 12 November 2011 Nucleic Acids Research, 2012, Vol. 40, Database issue D1211–D1215 doi:10.1093/nar/gkr1047 GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database Nils Kleinboelting, Gunnar Huep, Andreas Kloetgen, Prisca Viehoever and Bernd Weisshaar* Center for Biotechnology (CeBiTec), Bielefeld University, Universitaetsstrasse 25, D-33615 Bielefeld, Germany Received September 14, 2011; Revised October 24, 2011; Accepted October 25, 2011 ABSTRACT T-DNA insertion mutants are very valuable for reverse genetics in Arabidopsis thaliana. Several projects have generated large sequence-indexed collections of T-DNA insertion lines, of which GABI-Kat is the second largest resource worldwide. User access to the collection and its Flanking Sequence Tags (FSTs) is provided by the front end SimpleSearch (http://www.GABI-Kat.de). Several significant improvements have been implemented recently. The database now relies on the TAIRv10 genome sequence and annotation dataset. All FSTs have been newly mapped using an optimized procedure that leads to improved accuracy of inser- tion site predictions. A fraction of the collection with weak FST yield was re-analysed by generating new FSTs. Along with newly found predictions for older sequences about 20 000 new FSTs were included in the database. Information about groups of FSTs pointing to the same insertion site that is found in several lines but is real only in a single line are included, and many problematic FST-to-line links have been corrected using new wet-lab data. SimpleSearch currently contains data from 71 000 lines with predicted insertions covering 62.5% of the 27 206 nuclear protein coding genes, and offers in- sertion allele-specific data from 9545 confirmed lines that are available from the Nottingham Arabidopsis Stock Centre. INTRODUCTION Since the genome sequence of the model plant Arabidopsis thaliana was completed in the year 2000 (1), the determin- ation of gene function is a key task in the Arabidopsis research community. Insertional mutagenesis approaches have been proven to be a valuable tool for reverse genetics (2). Several large collections of A. thaliana lines containing independent insertions of Agrobacterium T-DNA in the plant genome have been established. T-DNA integration in the plant genome results in stable mutations, which may perturb gene functions. An import- ant goal is to saturate the A. thaliana genome with T-DNA insertion lines for each (or at least most) of the 27 206 nuclear protein-coding genes that are currently annotated (3). A popular strategy to determine the position of a T-DNA insertion in the genome of a given insertion line is to generate Flanking Sequence Tags (FSTs). Using PCR-based methods, genomic DNA fragments ﬂanking the T-DNA are ampliﬁed (4), sequenced and subsequently mapped to the genome. When this is applied to a large collection of lines, the population can easily be searched for mutants of interest. GABI-Kat is the second largest FST-indexed T-DNA insertion line collection of A. thaliana, which is publicly available since 2002 (5). User access to the collection and extensive metadata for the included mutants and alleles is provided by GABI-Kat SimpleSearch, the web interface of the corresponding database (6). The interface can either be used to search the collection for mutant alleles of interest, or more importantly to access different kinds of informa- tion about speciﬁc GABI-Kat lines. Lines containing in- sertions of interest can be ordered via a web order form, which is also provided in SimpleSearch. In contrast to other FST databases, GABI-Kat SimpleSearch offers in- formation on conﬁrmation success of lines along with se- quences derived from the T-DNA/genome junction of an offspring generation, segregation data and primer infor- mation for the respective insertions (7). Since its availability in 2002, the database as well as the interface has been continuously improved. However, during the last 18 months several signiﬁcant improvements and extensions have been implemented that are beneﬁcial for users that rely on SimpleSearch when working with GABI-Kat insertion alleles. These enhancements include an extended data set, allow an easier and more comfort- able user access, and provide more detailed and more *To whom correspondence should be addressed. Tel: +49 521 106 8720; Fax: +49 521 106 6423; Email: bernd.weisshaar@uni-bielefeld.de The authors wish it to be known that, in their opinion, the ﬁrst two authors should be regarded as joint First Authors. The Author(s) 2011. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.