FLAGdb++:: a database for the functional analysis of the Arabidopsis genome

被引：45

作者：

Samson, F ^{[1
]}

Brunaud, V ^{[1
]}

Duchêne, S ^{[1
]}

De Oliveira, Y ^{[1
]}

Caboche, M ^{[1
]}

Lecharny, A ^{[1
]}

Aubourg, S ^{[1
]}

机构：

[1] Univ Evry Val Essonne, CNRS 8114, UMR INRA 1165, URGV, F-91057 Evry, France

来源：

NUCLEIC ACIDS RESEARCH | 2004年 / 32卷

关键词：

D O I：

10.1093/nar/gkh134

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：

FLAGdb(++) is dedicated to the integration and visualization of data for high-throughput functional analysis of a fully sequenced genome, as-illustrated for Arabidopsis. FLAGdb(++) displays the predicted or experimental data in a position-dependent way and displays correlations and relationships between different features. FLAGdb(++) provides for a given genome region, summarized characteristics of experimental materials like probe lengths, locations and specificities having an impact upon the confidence we will put in the experimental results. A selected subset of the available information is linked to a locus represented on an easy-to-interpret and memorable graphical display. Data are curated, processed and formatted before their integration into FLAGdb(++). FLAGdb(++) contains different options for easy back and forth navigation through many loci selected at the start of a session. It includes an original two-component visualization of the data, a genome-wide and a local view, which are permanently linked and display complementary information. Density curves along the chromosomes may be displayed in parallel for suggesting correlations between different structural and functional data. FLAGdb(++) is fully accessible at http://genoplante-info.infobiogen.fr/FLAGdb/.

引用

页码：D347 / D350

页数：4

共 17 条

[1] 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

[2] Improved PCR-walking for large-scale isolation of plant T-DNA borders [J].

Balzergue, S ;

Dubreucq, B ;

Chauvin, S ;

Le-Clainche, I ;

Le Boulaire, F ;

de Rose, R ;

Samson, F ;

Biaudet, V ;

Lecharny, A ;

Cruaud, C ;

Weissenbach, J ;

Caboche, M ;

Lepiniec, L .

BIOTECHNIQUES, 2001, 30 (03) :496-+

[3]

Bateman A, 2004, NUCLEIC ACIDS RES, V32, pD138, DOI [10.1093/nar/gkp985, 10.1093/nar/gkr1065, 10.1093/nar/gkh121]

[4]

Berriman Matt, 2003, Briefings in Bioinformatics, V4, P124, DOI 10.1093/bib/4.2.124

[5]

BIAUDET V, 1998, MICROB COMP GENOMICS, V3, P71

[6] T-DNA integration into the Arabidopsis genome depends on sequences of pre-insertion sites [J].

Brunaud, V ;

Balzergue, S ;

Dubreucq, B ;

Aubourg, S ;

Samson, F ;

Chauvin, S ;

Bechtold, N ;

Cruaud, C ;

DeRose, R ;

Pelletier, G ;

Lepiniec, L ;

Caboche, M ;

Lecharny, A .

EMBO REPORTS, 2002, 3 (12) :1152-1157

[7] CATMA:: a complete Arabidopsis GST database [J].

Crowe, ML ;

Serizet, C ;

Thareau, V ;

Aubourg, S ;

Rouzé, P ;

Hilson, P ;

Beynon, J ;

Weisbeek, P ;

van Hummelen, P ;

Reymond, P ;

Paz-Ares, J ;

Nietfeld, W ;

Trick, M .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :156-158

[8] Whole-genome sequence annotation: 'Going wrong with confidence' [J].

Kyrpides, NC ;

Ouzounis, CA .

MOLECULAR MICROBIOLOGY, 1999, 32 (04) :886-887

[9] 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

[10] PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization [J].

Nakai, K ;

Horton, P .

TRENDS IN BIOCHEMICAL SCIENCES, 1999, 24 (01) :34-35

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