GABI-Kat SimpleSearch


22080561	GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database. [PMID: 22080561] Kleinboelting N, Huep G, Kloetgen A, Viehoever P, Weisshaar B. 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 insertion 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 insertion allele-specific data from 9545 confirmed lines that are available from the Nottingham Arabidopsis Stock Centre. Nucleic Acids Res. 2012:40(Database issue) \| 242 Citations (from Europe PMC, 2025-03-29)
17062622	GABI-Kat SimpleSearch: an Arabidopsis thaliana T-DNA mutant database with detailed information for confirmed insertions. [PMID: 17062622] Li Y, Rosso MG, Viehoever P, Weisshaar B. Abstract Insertional mutagenesis approaches, especially by T-DNA, play important roles in gene function studies of the model plant Arabidopsis thaliana. GABI-Kat SimpleSearch (http://www.GABI-Kat.de) is a Flanking Sequence Tag (FST)-based database for T-DNA insertion mutants generated by the GABI-Kat project. Currently, the database contains >108,000 mapped FSTs from approximately 64,000 lines which cover 64% of all annotated A.thaliana protein-coding genes. The web interface allows searching for relevant insertions by gene code, keyword, line identifier, GenBank accession number of the FST, and also by BLAST. A graphic display of the genome region around the gene or the FST assists users to select insertion lines of their interests. About 3500 insertions were confirmed in the offspring of the plant from which the original FST was generated, and the seeds of these lines are available from the Nottingham Arabidopsis Stock Centre. The database now also contains additional information such as segregation data, gene-specific primers and confirmation sequences. This information not only helps users to evaluate the usefulness of the mutant lines, but also covers a big part of the molecular characterization of the insertion alleles. Nucleic Acids Res. 2007:35(Database issue) \| 40 Citations (from Europe PMC, 2025-03-29)
12874060	GABI-Kat SimpleSearch: a flanking sequence tag (FST) database for the identification of T-DNA insertion mutants in Arabidopsis thaliana. [PMID: 12874060] Li Y, Rosso MG, Strizhov N, Viehoever P, Weisshaar B. Abstract GABI-Kat SimpleSearch is a database of flanking sequence tags (FSTs) of T-DNA mutagenized Arabidopsis thaliana lines that were generated by the GABI-Kat project. Sequences flanking the T-DNA insertion sites were aligned to the A.thaliana genome sequence, annotated with information about the FST, the insertion site and the line from which the FST was derived. A web interface permits text-based as well as sequence-based searches for relevant insertions. GABI-Kat SimpleSearch aims to help biologists to quickly find T-DNA insertion mutants for their research. http://www.mpiz-koeln.mpg.de/GABI-Kat/ Bioinformatics. 2003:19(11) \| 51 Citations (from Europe PMC, 2025-03-29)

GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database. [PMID: 22080561]

Kleinboelting N, Huep G, Kloetgen A, Viehoever P, Weisshaar B.

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 insertion 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 insertion allele-specific data from 9545 confirmed lines that are available from the Nottingham Arabidopsis Stock Centre.

Nucleic Acids Res. 2012:40(Database issue) | 242 Citations (from Europe PMC, 2025-03-29)

GABI-Kat SimpleSearch: an Arabidopsis thaliana T-DNA mutant database with detailed information for confirmed insertions. [PMID: 17062622]

Li Y, Rosso MG, Viehoever P, Weisshaar B.

Abstract

Insertional mutagenesis approaches, especially by T-DNA, play important roles in gene function studies of the model plant Arabidopsis thaliana. GABI-Kat SimpleSearch (http://www.GABI-Kat.de) is a Flanking Sequence Tag (FST)-based database for T-DNA insertion mutants generated by the GABI-Kat project. Currently, the database contains >108,000 mapped FSTs from approximately 64,000 lines which cover 64% of all annotated A.thaliana protein-coding genes. The web interface allows searching for relevant insertions by gene code, keyword, line identifier, GenBank accession number of the FST, and also by BLAST. A graphic display of the genome region around the gene or the FST assists users to select insertion lines of their interests. About 3500 insertions were confirmed in the offspring of the plant from which the original FST was generated, and the seeds of these lines are available from the Nottingham Arabidopsis Stock Centre. The database now also contains additional information such as segregation data, gene-specific primers and confirmation sequences. This information not only helps users to evaluate the usefulness of the mutant lines, but also covers a big part of the molecular characterization of the insertion alleles.

Nucleic Acids Res. 2007:35(Database issue) | 40 Citations (from Europe PMC, 2025-03-29)

GABI-Kat SimpleSearch: a flanking sequence tag (FST) database for the identification of T-DNA insertion mutants in Arabidopsis thaliana. [PMID: 12874060]

Li Y, Rosso MG, Strizhov N, Viehoever P, Weisshaar B.

Abstract

GABI-Kat SimpleSearch is a database of flanking sequence tags (FSTs) of T-DNA mutagenized Arabidopsis thaliana lines that were generated by the GABI-Kat project. Sequences flanking the T-DNA insertion sites were aligned to the A.thaliana genome sequence, annotated with information about the FST, the insertion site and the line from which the FST was derived. A web interface permits text-based as well as sequence-based searches for relevant insertions. GABI-Kat SimpleSearch aims to help biologists to quickly find T-DNA insertion mutants for their research. http://www.mpiz-koeln.mpg.de/GABI-Kat/

Bioinformatics. 2003:19(11) | 51 Citations (from Europe PMC, 2025-03-29)

URL:	http://www.gabi-kat.de/
Full name:	GABI-Kat SimpleSearch
Description:	GABI-Kat SimpleSearch is a database of flanking sequence tags (FSTs) of T-DNA mutagenized Arabidopsis thaliana lines that were generated by the GABI-Kat project.
Year founded:	2003
Last update:	5/29/2015
Version:
Accessibility:	Accessible
Country/Region:	Germany

Data type:	DNA
Data object:	Plant
Database category:	Genotype phenotype and variation
Major species:	Arabidopsis thaliana
Keywords:	Flanking Sequence Tag T-DNA insertion mutant

University/Institution:	Bielefeld University
Address:	Universitaetsstrasse 25,D-33615 Bielefeld,Germany
City:	Bielefeld
Province/State:
Country/Region:	Germany
Contact name (PI/Team):	Bernd Weisshaar
Contact email (PI/Helpdesk):	bernd.weisshaar@uni-bielefeld.de

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