Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

被引：8604

作者：

DeSantis, T. Z.

Hugenholtz, P.

Larsen, N.

Rojas, M.

Brodie, E. L.

Keller, K.

Huber, T.

Dalevi, D.

Hu, P.

Andersen, G. L.

机构：

[1] Lawrence Berkeley Natl Lab, Ctr Environm Biotechnol, Berkeley, CA 94720 USA

[2] DOE Joint Genome Inst, Microbiol Ecol Program, Walnut Creek, CA 94598 USA

[3] Danish Genome Inst, DK-8000 Aarhus, Denmark

[4] Baylor Univ, Dept Bioinformat, Waco, TX 76798 USA

[5] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA

[6] Univ Queensland, Dept Biochem, Brisbane, Qld 4072, Australia

[7] Univ Queensland, Dept Math, Brisbane, Qld 4072, Australia

[8] Chalmers Univ Technol, Dept Comp Sci, SE-41296 Gothenburg, Sweden

来源：

APPLIED AND ENVIRONMENTAL MICROBIOLOGY | 2006年 / 72卷 / 07期

关键词：

D O I：

10.1128/AEM.03006-05

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

A 16S rRNA gene database (http://greengenes.bl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.

引用

收藏

页码：5069 / 5072

页数：4

相关论文

共 30 条

[1] BASIC LOCAL ALIGNMENT SEARCH TOOL [J].

ALTSCHUL, SF ;

GISH, W ;

MILLER, W ;

MYERS, EW ;

LIPMAN, DJ .

JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410

[2] PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database [J].

Ashelford, KE ;

Weightman, AJ ;

Fry, JC .

NUCLEIC ACIDS RESEARCH, 2002, 30 (15) :3481-3489

[3] At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies [J].

Ashelford, KE ;

Chuzhanova, NA ;

Fry, JC ;

Jones, AJ ;

Weightman, AJ .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2005, 71 (12) :7724-7736

[4] Bacterial community dynamics across a floristic gradient in a temperate upland grassland ecosystem [J].

Brodie, E ;

Edwards, S ;

Clipson, N .

MICROBIAL ECOLOGY, 2002, 44 (03) :260-270

[5] Development of a universal microarray based on the ligation detection reaction and 16S rRNA gene polymorphism to target diversity of cyanobacteria [J].

Castiglioni, B ;

Rizzi, E ;

Frosini, A ;

Sivonen, K ;

Rajaniemi, P ;

Rantala, A ;

Mugnai, MA ;

Ventura, S ;

Wilmotte, A ;

Boutte, C ;

Grubisic, S ;

Balthasart, P ;

Consolandi, C ;

Bordoni, R ;

Mezzelani, A ;

Battaglia, C ;

De Bellis, G .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2004, 70 (12) :7161-7172

[6] The Jalview Java']Java alignment editor [J].

Clamp, M ;

Cuff, J ;

Searle, SM ;

Barton, GJ .

BIOINFORMATICS, 2004, 20 (03) :426-427

[7] The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis [J].

Cole, JR ;

Chai, B ;

Farris, RJ ;

Wang, Q ;

Kulam, SA ;

McGarrell, DM ;

Garrity, GM ;

Tiedje, JM .

NUCLEIC ACIDS RESEARCH, 2005, 33 :D294-D296

[8] Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray [J].

DeSantis, TZ ;

Stone, CE ;

Murray, SR ;

Moberg, JP ;

Andersen, GL .

FEMS MICROBIOLOGY LETTERS, 2005, 245 (02) :271-278

[9] Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA [J].

DeSantis, TZ ;

Dubosarskiy, I ;

Murray, SR ;

Andersen, GL .

BIOINFORMATICS, 2003, 19 (12) :1461-1468

[10]

DESANTIS TZ, IN PRESS NUCL ACIDS