GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database

被引:283
作者
Kleinboelting, Nils [1 ]
Huep, Gunnar [1 ]
Kloetgen, Andreas [1 ]
Viehoever, Prisca [1 ]
Weisshaar, Bernd [1 ]
机构
[1] Univ Bielefeld, Ctr Biotechnol CeBiTec, D-33615 Bielefeld, Germany
关键词
INFORMATION; GENERATION;
D O I
10.1093/nar/gkr1047
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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 similar to 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.
引用
收藏
页码:D1211 / D1215
页数:5
相关论文
共 13 条
[1]   Genome-wide Insertional mutagenesis of Arabidopsis thaliana [J].
Alonso, JM ;
Stepanova, AN ;
Leisse, TJ ;
Kim, CJ ;
Chen, HM ;
Shinn, P ;
Stevenson, DK ;
Zimmerman, J ;
Barajas, P ;
Cheuk, R ;
Gadrinab, C ;
Heller, C ;
Jeske, A ;
Koesema, E ;
Meyers, CC ;
Parker, H ;
Prednis, L ;
Ansari, Y ;
Choy, N ;
Deen, H ;
Geralt, M ;
Hazari, N ;
Hom, E ;
Karnes, M ;
Mulholland, C ;
Ndubaku, R ;
Schmidt, I ;
Guzman, P ;
Aguilar-Henonin, L ;
Schmid, M ;
Weigel, D ;
Carter, DE ;
Marchand, T ;
Risseeuw, E ;
Brogden, D ;
Zeko, A ;
Crosby, WL ;
Berry, CC ;
Ecker, JR .
SCIENCE, 2003, 301 (5633) :653-657
[2]   Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].
Altschul, SF ;
Madden, TL ;
Schaffer, AA ;
Zhang, JH ;
Zhang, Z ;
Miller, W ;
Lipman, DJ .
NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402
[3]   Analysis of the genome sequence of the flowering plant Arabidopsis thaliana [J].
Kaul, S ;
Koo, HL ;
Jenkins, J ;
Rizzo, M ;
Rooney, T ;
Tallon, LJ ;
Feldblyum, T ;
Nierman, W ;
Benito, MI ;
Lin, XY ;
Town, CD ;
Venter, JC ;
Fraser, CM ;
Tabata, S ;
Nakamura, Y ;
Kaneko, T ;
Sato, S ;
Asamizu, E ;
Kato, T ;
Kotani, H ;
Sasamoto, S ;
Ecker, JR ;
Theologis, A ;
Federspiel, NA ;
Palm, CJ ;
Osborne, BI ;
Shinn, P ;
Conway, AB ;
Vysotskaia, VS ;
Dewar, K ;
Conn, L ;
Lenz, CA ;
Kim, CJ ;
Hansen, NF ;
Liu, SX ;
Buehler, E ;
Altafi, H ;
Sakano, H ;
Dunn, P ;
Lam, B ;
Pham, PK ;
Chao, Q ;
Nguyen, M ;
Yu, GX ;
Chen, HM ;
Southwick, A ;
Lee, JM ;
Miranda, M ;
Toriumi, MJ ;
Davis, RW .
NATURE, 2000, 408 (6814) :796-815
[4]   A new DNA sequence assembly program [J].
Bonfield, JK ;
Smith, KF ;
Staden, R .
NUCLEIC ACIDS RESEARCH, 1995, 23 (24) :4992-4999
[5]   GABI-Kat SimpleSearch: a flanking sequence tag (FST) database for the identification of T-DNA insertion mutants in Arabidopsis thaliana [J].
Li, Y ;
Rosso, MG ;
Strizhov, N ;
Viehoever, P ;
Weisshaar, B .
BIOINFORMATICS, 2003, 19 (11) :1441-1442
[6]   GABI-Kat SimpleSearch:: an Arabidopsis thaliana T-DNA mutant database with detailed information for confirmed insertions [J].
Li, Yong ;
Rosso, Mario G. ;
Viehoever, Prisca ;
Weisshaar, Bernd .
NUCLEIC ACIDS RESEARCH, 2007, 35 :D874-D878
[7]   Linking genotype to phenotype using the Arabidopsis unimutant collection [J].
O'Malley, Ronan C. ;
Ecker, Joseph R. .
PLANT JOURNAL, 2010, 61 (06) :928-940
[8]   An Arabidopsis thaliana T-DNA mutagenized population (GABI-Kat) for flanking sequence tag-based reverse genetics [J].
Rosso, MG ;
Li, Y ;
Strizhov, N ;
Reiss, B ;
Dekker, K ;
Weisshaar, B .
PLANT MOLECULAR BIOLOGY, 2003, 53 (01) :247-259
[9]   FLAGdb++:: a database for the functional analysis of the Arabidopsis genome [J].
Samson, F ;
Brunaud, V ;
Duchêne, S ;
De Oliveira, Y ;
Caboche, M ;
Lecharny, A ;
Aubourg, S .
NUCLEIC ACIDS RESEARCH, 2004, 32 :D347-D350
[10]  
Staden R, 2000, Methods Mol Biol, V132, P115