Journal Article

Rice TOGO Browser: A Platform to Retrieve Integrated Information on Rice Functional and Applied Genomics

Yoshiaki Nagamura, Baltazar A. Antonio, Yutaka Sato, Akio Miyao, Nobukazu Namiki, Jun-ichi Yonemaru, Hiroshi Minami, Kaori Kamatsuki, Kan Shimura, Yuji Shimizu and Hirohiko Hirochika

in Plant and Cell Physiology

Published on behalf of Japanese Society of Plant Physiologists

Volume 52, issue 2, pages 230-237
Published in print February 2011 | ISSN: 0032-0781
Published online January 2011 | e-ISSN: 1471-9053 | DOI: http://dx.doi.org/10.1093/pcp/pcq197

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  • Biochemistry
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The Rice TOGO Browser is an online public resource designed to facilitate integration and visualization of mapping data of bacterial artificial chromosome (BAC)/P1-derived artificial chromosome (PAC) clones, genes, restriction fragment length polymorphism (RFLP)/simple sequence repeat (SSR) markers and phenotype data represented as quantitative trait loci (QTLs) onto the genome sequence, and to provide a platform for more efficient utilization of genome information from the point of view of applied genomics as well as functional genomics. Three search options, namely keyword search, region search and trait search, generate various types of data in a user-friendly interface with three distinct viewers, a chromosome viewer, an integrated map viewer and a sequence viewer, thereby providing the opportunity to view the position of genes and/or QTLs at the chromosomal level and to retrieve any sequence information in a user-defined genome region. Furthermore, the gene list, marker list and genome sequence in a specified region delineated by RFLP/SSR markers and any sequences designed as primers can be viewed and downloaded to support forward genetics approaches. An additional feature of this database is the graphical viewer for BLAST search to reveal information not only for regions with significant sequence similarity but also for regions adjacent to those with similarity but with no hits between sequences. An easy to use and intuitive user interface can help a wide range of users in retrieving integrated mapping information including agronomically important traits on the rice genome sequence. The database can be accessed at http://agri-trait.dna.affrc.go.jp/.

Keywords: Applied genomics; BLAST; Database; Functional genomics; Rice; Structural genomics

Journal Article.  3287 words.  Illustrated.

Subjects: Biochemistry ; Molecular and Cell Biology ; Plant Sciences and Forestry

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