Unified display of Arabidopsis thaliana physical maps from AtDB, the A.thaliana database

In the past several years, there has been a tremendous effort to construct physical maps and to sequence the genome of Arabidopsis thaliana. As a result, four of the five chromosomes are completely covered by overlapping clones except at the centromeric and nucleolus organizer regions (NOR). In addition, over 30% of the genome has been sequenced and completion is anticipated by the end of the year 2000. Despite these accomplishments, the physical maps are provided in many formats on laboratories' Web sites. These data are thus difficult to obtain in a coherent manner for researchers. To alleviate this problem, AtDB (Arabidopsis thaliana DataBase, URL: http://genome-www.stanford.edu/Arabidopsis/) has constructed a unified display of the physical maps where all publicly available physical-map data for all chromosomes are presented through the Web in a clickable, 'on-the-fly' graphic, created by CGI programs that directly consult our relational database.

[1]  C. Dean,et al.  Description of 31 YAC contigs spanning the majority of Arabidopsis thaliana chromosome 5. , 1997, The Plant journal : for cell and molecular biology.

[2]  H. Goodman,et al.  Construction of an ∼2 Mb contig in the region around 80 cM of Arabidopsis thaliana chromosome 2 , 1997 .

[3]  A Grigoriev,et al.  Algorithms and software tools for ordering clone libraries: application to the mapping of the genome of Schizosaccharomyces pombe. , 1993, Nucleic acids research.

[4]  P. Piffanelli,et al.  Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana , 1998, Nature.

[5]  J. Cherry,et al.  Arabidopsis thaliana: a model plant for genome analysis. , 1998, Science.

[6]  D. Shibata,et al.  A fine physical map of Arabidopsis thaliana chromosome 5: construction of a sequence-ready contig map. , 1997, DNA research : an international journal for rapid publication of reports on genes and genomes.

[7]  C. Dean,et al.  Detailed description of four YAC contigs representing 17 Mb of chromosome 4 of Arabidopsis thaliana ecotype Columbia. , 1996, The Plant journal : for cell and molecular biology.

[8]  C. Camilleri,et al.  A YAC contig map of Arabidopsis thaliana chromosome 3. , 1998, The Plant journal : for cell and molecular biology.

[9]  Kevin A. Pyke.  Arabidopsis: annual plant reviews, volume 1. (Ed. by MARY ANDERSON and JEREMY A. ROBERTS.) 24×16 cm. Pp. 407. Sheffield, UK: Sheffield Academic Press. Price h/b: £95.00. ISBN 1 85075 8905. , 1999 .

[10]  Y. Nakamura,et al.  Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence features of the 1.6 Mb regions covered by twenty physically assigned P1 clones. , 1997, DNA research : an international journal for rapid publication of reports on genes and genomes.

[11]  Shuai Weng,et al.  AtDB, the Arabidopsis thaliana database, and graphical-web-display of progress by the Arabidopsis Genome Initiative , 1998, Nucleic Acids Res..

[12]  H. Goodman,et al.  A physical map of chromosome 2 of Arabidopsis thaliana. , 1996, Genome research.

[13]  D. Shibata,et al.  A physical map of Arabidopsis thaliana chromosome 3 represented by two contigs of CIC YAC, P1, TAC and BAC clones. , 1998, DNA research : an international journal for rapid publication of reports on genes and genomes.